Microorganisms for producing organic acids

ABSTRACT

Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. patent application Ser. No. 13/798,835, filed Mar. 13, 2013, and claims priority under 35 USC §119(e) to U.S. Provisional Patent Application 61/647,001 filed May 15, 2012, the entireties of which are incorporated herein by reference. This application incorporates by reference co-filed U.S. patent application Ser. No. 14,200,747, which is also a continuation in-part of U.S. patent application Ser. No. 13/798,835, filed Mar. 13, 2013, and claim priority under 35 USC §119(e) to U.S. Provisional Patent Application 61,647,001 filed May 15, 2012.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under FA9550-11-1-0038 awarded by the USAF/AFOSR, DE-FC02-07ER64494 awarded by the US Department of Energy, and 1240268 awarded by the National Science Foundation. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to organic acid-tolerant microorganisms capable of producing organic acids and uses thereof for producing organic acids.

BACKGROUND

Production of industrially useful chemicals has conventionally focused on the use of petroleum-like compounds as starting materials. However, various factors have increased interest in the production of such chemicals through microorganism-mediated bioconversion of biomass and other renewable resources.

Accordingly, the U.S. Department of Energy (DOE) recently identified several “building block” chemicals to be produced via microorganism consumption of biomass. The identified chemicals include 1,4 succinic acid, fumaric and malic acids, 2,5 furan dicarboxylic acid, 3-hydroxypropionic acid (3HP), aspartic acid, glucaric acid, glutamic acid, itaconic acid, levulinic acid, 3-hydroxybutyrolactone, glycerol, sorbitol, and xylitol/arabinitol. These chemicals can be converted to high-value, bio-based chemicals or materials.

As an example, 3HP can be readily transformed into a variety of commodity chemicals such as acrylic acid, methyl acrylate, and 1,3-propanediol. These commodity chemicals represent a multi-billion dollar a year industry and are used in the production of plastics, coatings, and fibers. U.S. demand for acrylic acid in particular is growing, exceeding 1×10⁹ kg/year. The current means of synthesizing acrylic acid include oxidation of propylene. A thermodynamically favorable pathway for microbial production of acrylic acid has not been identified.

One hurdle facing the microbial production of industrially useful chemicals is that many, including 3HP, are toxic to the microbes capable of producing them. Recently, efforts have been made not only to increase microbial output of the chemicals but also to increase microbial tolerance to the chemicals. Some of these efforts have focused on the production of 3HP in the heterotrophic microbe Escherichia coli. See, e.g., U.S. Pat. No. 8,048,624 to Lynch, U.S. Pub. 2011/0125118 to Lynch, U.S. Pub. 2010/0210017 to Gill et al., and Warnecke et al. Metabolic Engineering (2010) 12:241-250.

While focusing on chemical production in heterotrophic microorganisms is a valuable strategy, a potential problem is the availability of carbon and energy sources such as food-based commodities and/or sugars derived from lignocellulosic biomass. An attractive alternative is to use phototrophic microorganisms, such as cyanobacteria. These microorganisms can produce chemical products from CO₂ and light energy without relying on consumption of higher-value carbon sources that can be used for other purposes, such as producing food, fuel, or other certain chemicals.

There is a need for microorganisms capable of producing high yields of industrially useful chemicals and having increased tolerance against those chemicals. There is also a need for microorganisms that use non-food-based feedstock in such production.

SUMMARY OF THE INVENTION

The present invention addresses the aforementioned needs by providing microorganisms with increased tolerance to organic acids. The present invention also provides microorganisms modified to produce organic acids. Methods of producing organic acids with the microorganisms described herein are also provided.

A preferred version of the invention comprises an organic acid-tolerant microorganism that includes a modification that reduces or ablates AcsA activity or AcsA homolog activity in the microorganism. The modification confers an increased tolerance to organic acids compared to a corresponding microorganism not comprising the modification.

The modification is preferably a genetic modification. The genetic modification is preferably a genetic modification other than or in addition to one resulting in a W49L substitution in AcsA or a corresponding substitution in an AcsA homolog.

The microorganism is preferably a bacterium, more preferably a cyanobacterium, and most preferably a cyanobacterium selected from the group consisting of Synechococcus sp., Prochlorococcus sp., Synechocystis sp., and Nostoc sp.

The tolerance to the organic acid is preferably increased at least about 25-fold in the microorganism of the invention compared to a corresponding microorganism.

In preferred versions of the invention, the microorganism is further modified to increase production of an organic acid. The microorganism may be modified to increase production of 3-hydroxypropionic acid, lactic acid, and/or others.

A microorganism of the invention modified to increase production of 3-hydroxyprionic acid preferably comprises one or more recombinant nucleic acids configured to express an enzyme selected from the group consisting of a malonyl-CoA reductase and a malonate semialdehyde reductase, wherein the microorganism produces an increased amount of 3-hydroxypropionic acid compared to a corresponding microorganism not comprising the one or more recombinant nucleic acids.

The malonyl-CoA reductase is preferably a malonyl-CoA reductase from Sulfolobus tokodaii or a homolog thereof. The malonyl-CoA reductase from Sulfolobus tokodaii or the homolog thereof preferably comprises an amino acid sequence at least about 80% identical, more preferably at least about 90% identical, and most preferably at least about 95% identical to SEQ ID NO:13.

The malonate semialdehyde reductase is preferably a malonate semialdehyde reductase from Metallosphaera sedula or a homolog thereof. The malonate semialdehyde reductase from Metallosphaera sedula or the homolog thereof preferably comprises an amino acid sequence at least about 80% identical, more preferably at least about 90% identical, and most preferably at least about 95% identical to SEQ ID NO:16.

A microorganism of the invention modified to increase production of lactic acid preferably comprises one or more recombinant nucleic acids configured to express an enzyme selected from the group consisting of a lactate dehydrogenase and a pyridine nucleotide transhydrogenase, wherein the microorganism produces an increased amount of lactic acid compared to a corresponding microorganism not comprising the one or more recombinant nucleic acids.

The lactate dehydrogenase is may be a lactate dehydrogenase from Bacillus subtilis or a homolog thereof. The lactate dehydrogenase from Bacillus subtilis or the homolog thereof preferably comprises an amino acid sequence at least about 80% identical, more preferably at least about 90% identical, and most preferably at least about 95% identical to SEQ ID NO:18.

The lactate dehydrogenase is may also or alternatively be a lactate dehydrogenase from Lactococcus lactis or a homolog thereof. The lactate dehydrogenase from Lactococcus lactis or the homolog thereof preferably comprises an amino acid sequence at least about 80% identical, more preferably at least about 90% identical, and most preferably at least about 95% identical to SEQ ID NO:22.

The pyridine nucleotide transhydrogenase is preferably a soluble pyridine nucleotide transhydrogenase from Escherichia coli or a homolog thereof. The soluble pyridine nucleotide transhydrogenase from Escherichia coli or the homolog thereof preferably comprises an amino acid sequence at least about 80% identical, more preferably at least about 90% identical, and most preferably at least about 95% identical to SEQ ID NO:20.

The invention further provides methods of producing an organic acid. The methods comprise culturing one of the microorganisms as described herein.

The objects and advantages of the invention will appear more fully from the following detailed description of the preferred embodiment of the invention made in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A depicts a schema for using acsA or a homolog thereof as a selection marker for introducing a DNA fragment of interest into the acsA or homolog chromosomal locus.

FIG. 1B depicts a schema for using acsA or a homolog thereof as a selection marker for introducing a DNA fragment of interest into a locus other than the acsA or homolog chromosomal locus.

FIG. 2A depicts growth of Synechococcus sp. PCC 7002 at OD730 as a function of time in the presence of 5 mM dimethylsulfoniopropionate (DMSP).

FIG. 2B depicts growth of Synechococcus sp. PCC 7002 at OD730 as a function of time in the presence of 5 mM acrylic acid.

FIG. 2C depicts growth of a mutant pool of Synechococcus sp. PCC 7002 at OD730 as a function of time in the presence of 5 mM dimethylsulfoniopropionate (DMSP) and 5 mM acrylic acid.

FIG. 3 depicts acrylate production from DMSP as a function of time for Synechococcus sp. PCC 7002 and an abiotic control.

FIG. 4A depicts growth of BPSyn_(—)006 (a ΔacsA strain of Synechococcus sp. PCC 7002 having a barcode sequence in place of the acsA gene (PCC 7002 acsA::BC)) and pH as a function of time in CO₂-limited conditions. Cultivation of BPSyn_(—)006 with 5 mM DMSP under CO₂-limited conditions results in an increase in pH over time.

FIG. 4B depicts acrylic acid accumulation over time from cultivation of BPSyn_(—)006 with 5 mM DMSP and abiotic controls with 5 mM DMSP at pH 8.0, 8.25, and 8.5. The rate of DMSP degradation to acrylic acid increases with an increase in pH.

FIG. 5 depicts plating of wild-type Synechococcus sp. PCC 7002, a mutant generated from growth in the presence of acrylic acid, a ΔacsA mutant, a ΔacsA mutant comprising the pAQ1 plasmid containing acsAW49L, and a ΔacsA mutant comprising the pAQ1 plasmid containing acsA on media containing no organic acid, 5 mM acrylic acid, or 30 mM 3-hydroxypropionic acid (3HP).

FIG. 6 depicts relative acyl-CoA ligase activity of AcsA for acetate, acrylate, propionate, and 3-hydroxypropionate (3HP).

FIG. 7 depicts two 3HP-production pathways, wherein 1 represents pyruvate kinase, 2 represents pyruvate dehydrogenase, 3 represents acetyl-CoA carboxylase, 4 represents malonyl-CoA reductase, 5 represents phosphoenolpyruvate carboxylase, 6 represents aspartate aminotransferase, 7 represents aspartate decarboxylase, and 8 represents β-alanine/α-ketoglutarate aminotransferase.

FIG. 8A depicts the percent of colonies positive for yellow fluorescent protein (YFP) or a barcode sequence resulting from use of acsA as a counter selection marker upon introducing the YFP or the barcode sequence into the chromosomal acsA locus of Synechococcus sp. PCC 7002.

FIG. 8B depicts levels of YFP expression from cells in which YFP was introduced into the glpK chromosomal locus using acsA as a counter selection marker and cells in which YFP was introduced into the acsA chromosomal locus using acsA as a counter selection marker.

FIG. 9A depicts a schema of the production of 3HP from CO₂ and photons (sunlight) in cyanobacteria. FIG. 9B depicts a schema of the production of 3HP from acetyl-CoA, showing the malonyl-CoA reductase and the malonate semialdehyde reductase steps in detail. “AccABCD” represents acetyl-CoA carboxylase. “MCR” represents malonyl-CoA reductase. “MSR” represents malonate semialdehyde reductase. “AcsA” represents acetyl-CoA synthetase.

FIG. 10 depicts an artificial operon construct configured to express malonyl-CoA reductase and malonate semialdehyde reductase. “p_(cpc)BLacOO” represents a LacI-regulatable promoter based on the cyanobacterial cpcB gene promoter. “RBS” represents a ribosome binding site. “MCR” represents a malonyl-CoA reductase coding sequence. “MSR” represents a malonate semialdehyde reductase coding sequence. “LacI” represents a gene for the lac repressor (Lad).

FIG. 11 depicts growth in the presence and absence of 1 mM IPTG as a function of time for Synechococcus sp. PCC 7002 lacking acsA and comprising the construct depicted in FIG. 10.

FIG. 12A depicts a schema for the production of lactate from pyruvate as catalyzed by lactate dehydrogenase (Ldh).

FIG. 12B depicts an equation of the reaction catalyzed by pyridine nucleotide transhydrogenase.

FIG. 13 depicts growth and lactate production in the presence and absence of 1 mM IPTG as a function of time for Synechococcus sp. PCC 7002 lacking acsA and comprising an IPTG-inducible lactate dehydrogenase gene with a coding sequence (ldh) from Bacillus subtilis.

FIG. 14 depicts growth and lactate production in the presence of 1 mM IPTG as a function of time for Synechococcus sp. PCC 7002 lacking acsA, comprising an IPTG-inducible lactate dehydrogenase gene with a coding sequence (ldh) derived from Bacillus subtilis, and comprising a soluble pyridine nucleotide transhydrogenase gene with a coding sequence (udhA) derived from Escherichia coli.

DETAILED DESCRIPTION OF THE INVENTION

One version of the invention includes a microorganism wherein an acsA gene product or homolog thereof is functionally deleted. The acsA gene product (AcsA) and homologs thereof are acetyl-CoA synthetases classified under Enzyme Commission (EC) number 6.2.1.1. Other names for these acetyl-CoA synthetases include “acetate-CoA ligases,” “acetyl-CoA ligases,” and “acyl-activating enzymes.”

“Functional deletion” or its grammatical equivalents refers to any modification to a microorganism that ablates, reduces, inhibits, or otherwise disrupts production of a gene product, renders the gene product non-functional, or otherwise reduces or ablates the gene product's activity. “Gene product” refers to a protein or polypeptide encoded and produced by a particular gene. “Gene” as used herein refers to a nucleic acid sequence capable of producing a gene product and may include such genetic elements as a coding sequence together with any other genetic elements required for transcription and/or translation of the coding sequence. Such genetic elements may include a promoter, an enhancer, and/or a ribosome binding site (RBS), among others. In some versions of the invention, “functionally deleted acsA gene product or homolog thereof” means that the acsA gene is mutated to an extent that an acsA gene product or homolog thereof is not produced at all.

One of ordinary skill in the art will appreciate that there are many well-known ways to functionally delete a gene product. For example, functional deletion can be accomplished by introducing one or more genetic modifications. As used herein, “genetic modifications” refer to any differences in the nucleic acid composition of a cell, whether in the cell's native chromosome or in endogenous or exogenous non-chromosomal plasmids harbored within the cell. Examples of genetic modifications that may result in a functionally deleted gene product include but are not limited to mutations, partial or complete deletions, insertions, or other variations to a coding sequence or a sequence controlling the transcription or translation of a coding sequence; placing a coding sequence under the control of a less active promoter; blocking transcription of the gene with a trans-acting DNA binding protein such as a TAL effector or CRISPR guided Cas9; and expressing ribozymes or antisense sequences that target the mRNA of the gene of interest, etc. In some versions, a gene or coding sequence can be replaced with a selection marker or screenable marker. Various methods for introducing the genetic modifications described above are well known in the art and include homologous recombination, among other mechanisms. See, e.g., Green et al., Molecular Cloning: A laboratory manual, 4^(th) ed., Cold Spring Harbor Laboratory Press (2012) and Sambrook et al., Molecular Cloning: A Laboratory Manual, 3^(rd) ed., Cold Spring Harbor Laboratory Press (2001). Various other genetic modifications that functionally delete a gene product are described in the examples below. Functional deletion can also be accomplished by inhibiting the activity of the gene product, for example, by chemically inhibiting a gene product with a small molecule inhibitor, by expressing a protein that interferes with the activity of the gene product, or by other means.

In certain versions of the invention, the functionally deleted gene product may have less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 1%, or about 0% of the activity of the non-functionally deleted gene product.

In certain versions of the invention, a cell with a functionally deleted gene product may have less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 1%, or about 0% of the activity of the gene product compared to a cell with the non-functionally deleted gene product.

In certain versions of the invention, the functionally deleted gene product may be expressed at an amount less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 1%, or about 0% of the amount of the non-functionally deleted gene product.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 30, at least 40, at least 50, or more nonsynonymous substitutions are present in the gene or coding sequence of the gene product.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 30, at least 40, at least 50, or more bases are inserted in the gene or coding sequence of the gene product.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of the gene product's gene or coding sequence is deleted or mutated.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of a promoter driving expression of the gene product is deleted or mutated.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of an enhancer controlling transcription of the gene product's gene is deleted or mutated.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of a sequence controlling translation of gene product's mRNA is deleted or mutated.

In certain versions of the invention, the decreased activity or expression of the functionally deleted gene product is determined with respect to the activity or expression of the gene product in its unaltered state as found in nature. In certain versions of the invention, the decreased activity or expression of the functionally deleted gene product is determined with respect to the activity or expression of the gene product in its form in a corresponding microorganism. In certain versions, the genetic modifications giving rise to a functionally deleted gene product are determined with respect to the gene or coding sequence in its unaltered state as found in nature. In certain versions, the genetic modifications giving rise to a functionally deleted gene product are determined with respect to the gene or coding sequence in its form in a corresponding microorganism.

Some versions of the invention include a plurality of microorganisms, wherein greater than about 1%, about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or more of the plurality of microorganisms comprise a functionally deleted acsA gene product or homolog thereof. In some versions, the plurality of microorganisms is a microbial culture.

Genetic modifications that can be introduced into the acsA gene or homologs thereof to functionally delete the acsA gene product or homologs thereof, such as generating acsA knockouts, are described in the examples below.

The acsA gene is an acetyl-CoA synthetase gene in the exemplary cyanobacterium Synechococcus sp. PCC 7002, the coding sequence of which can be found in GenBank under accession number NC_(—)010475.1 and is as follows:

(SEQ ID NO: 1) atgtccgaac aaaacattga atccatcctc caggagcagc  gccttttttc gcctgcacca gactttgctg ccgaggccca   gatcaagagc ttagaccagt accaagccct ctacgaccgg    gcgaaaaatg accccgaagg cttttggggg gaactcgccg   aacaggaatt ggaatggttt gagaaatggg acaaggtgct cgattggcaa ccgcccttcg ccaaatggtt tgtcaacggg  aaaattaaca tttcctacaa ttgcctcgac cgtcatctca  aaacctggcg caaaaataaa gccgccctca tctgggaagg ggaacccggt gactcccgta ccctcaccta tgcccagcta caccacgagg tctgccagtt tgccaatgcg atgaaaaagt tgggcgtcaa aaaaggcgat cgcgtcggga tttatatgcc  aatgatcccg gaagccgtcg ttgccctcct cgcctgtgcc  cgcattggtg cgccccatac ggtgatattt ggtggcttta gtgccgaagc cctccgcagt cgcctcgaag acgctgaagc caaactggtg atcaccgccg acgggggctt ccgcaaagat aaagcggtac ccctcaagga tcaagtagat gcggcgatcg  ccgatcacca tgcccccagc gttgagaatg ttttggtcgt tcaacgcacc aaagagcctg tccacatgga agccgggcgg gatcactggt ggcatgattt gcaaaaagaa gtctccgctg actgtcccgc cgagccgatg gatgccgaag atatgctctt catcctctat accagcggca ccacgggtaa acccaagggc  gttgtccaca ctacgggcgg ttataatctc tacacccata taacgaccaa gtggatcttt gatctcaaag atgatgacgt gtattggtgt ggtgctgatg tgggttggat caccggccac agttacatta cctatggccc tctatctaac ggggcaacgg tcttaatgta tgaaggcgca ccccgtccgt ctaatcccgg  ttgctattgg gaaattattc aaaaatatgg tgtcaccatt  ttctatacgg cacccacagc gattcgggcc tttatcaaaa tgggtgaagg catccccaat aaatatgaca tgagttccct gcgcctctta ggaaccgtgg gtgaaccgat taacccagaa gcttggatgt ggtaccaccg ggtcattggt ggcgaacgtt  gtcccattgt tgatacatgg tggcaaacgg aaaccggtgg  tgtgatgatt acgcctttac ccggtgcaac tcccacaaaa cccggctcgg caactcgtcc ttttccgggg attgtggcgg atgtcgttga ccttgatgga aattccgttg gtgacaacga aggcggctac ctggtagtga aacaaccctg gcctgggatg  atgcgtactg tttacggcaa tcccgaacgc ttccggtcta  cctattggga gcacatcgcc ccgaaagatg gacaatacct ttatttcgca ggtgacgggg cacgccgtga ccaagatggc tatttttgga ttatgggtcg cgtcgatgat gtcttaaatg tttcgggcca tcgcctcggc accatggaag tggaatcggc  cctcgtttcc caccctgccg tcgccgaagc agccgtggtt ggaaagccag atccggttaa gggggaagag gtgtttgcct ttgtcaccct tgagggcacc tacagtccga gcgacgatct cgtaacggaa ctcaaggccc atgtggtgaa agaaattggg gcgatcgccc gtccgggaga aatccgtttt gccgatgtaa  tgcccaaaac ccgttctggg aagatcatgc ggcgtttgtt  gcgaaaccta gccgcaggtc aggaaattgt gggcgacacc  tccaccctcg aagaccgcag cgtcctcgat caactccggg   gctaa The acsA coding sequence in the exemplary organism Synechococcus sp. PCC 7002 encodes a protein included in GenBank under accession number YP_(—)001735082.1, having the following amino acid sequence:

(SEQ ID NO: 2) MSEQNIESIL QEQRLFSPAP DFAAEAQIKS LDQYQALYDR  AKNDPEGFWG ELAEQELEWF EKWDKVLDWQ PPFAKWFVNG KINISYNCLD RHLKTWRKNK AALIWEGEPG DSRTLTYAQL HHEVCQFANA MKKLGVKKGD RVGIYMPMIP EAVVALLACA RIGAPHTVIF GGFSAEALRS RLEDAEAKLV ITADGGFRKD KAVPLKDQVD AAIADHHAPS VENVLVVQRT KEPVHMEAGR  DHWWHDLQKE VSADCPAEPM DAEDMLFILY TSGTTGKPKG VVHTTGGYNL YTHITTKWIF DLKDDDVYWC GADVGWITGH SYITYGPLSN GATVLMYEGA PRPSNPGCYW EIIQKYGVTI FYTAPTAIRA FIKMGEGIPN KYDMSSLRLL GTVGEPINPE AWMWYHRVIG GERCPIVDTW WQTETGGVMI TPLPGATPTK  PGSATRPFPG IVADVVDLDG NSVGDNEGGY LVVKQPWPGM MRTVYGNPER FRSTYWEHIA PKDGQYLYFA GDGARRDQDG YFWIMGRVDD VLNVSGHRLG TMEVESALVS HPAVAEAAVV GKPDPVKGEE VFAFVTLEGT YSPSDDLVTE LKAHVVKEIG AIARPGEIRF ADVMPKTRSG KIMRRLLRNL AAGQEIVGDT  STLEDRSVLD QLRG

Homologs of acsA include coding sequences, genes, or gene products that are homologous to the acsA coding sequence, acsA gene, or the acsA gene product, respectively. Proteins and/or protein sequences are “homologous” when they are derived, naturally or artificially, from a common ancestral protein or protein sequence. Similarly, nucleic acids and/or nucleic acid sequences are homologous when they are derived, naturally or artificially, from a common ancestral nucleic acid or nucleic acid sequence. Homology is generally inferred from sequence similarity between two or more nucleic acids or proteins (or sequences thereof). The precise percentage of similarity between sequences that is useful in establishing homology varies with the nucleic acid and protein at issue, but as little as 25% sequence similarity (e.g., identity) over 50, 100, 150 or more residues (nucleotides or amino acids) is routinely used to establish homology (e.g., over the full length of the two sequences to be compared). Higher levels of sequence similarity (e.g., identity), e.g., 30%, 35% 40%, 45% 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% or more, can also be used to establish homology. Accordingly, homologs of the coding sequences, genes, or gene products described herein include coding sequences, genes, or gene products, respectively, having at least about 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to the coding sequences, genes, or gene products described herein. Methods for determining sequence similarity percentages (e.g., BLASTP and BLASTN using default parameters) are described herein and are generally available. The homologous proteins should demonstrate comparable activities and, if an enzyme, participate in the same or analogous pathways. “Orthologs” are genes or coding sequences thereof in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same or similar function in the course of evolution. As used herein “orthologs” are included in the term “homologs”.

For sequence comparison and homology determination, one sequence typically acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence based on the designated program parameters. A typical reference sequence of the invention is a nucleic acid or amino acid sequence corresponding to acsA or other coding sequences, genes, or gene products described herein.

Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2008)).

One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity for purposes of defining homologs is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always<0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).

In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001. The above-described techniques are useful in identifying homologous sequences for use in the methods described herein.

The terms “identical” or “percent identity”, in the context of two or more nucleic acid or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described above (or other algorithms available to persons of skill) or by visual inspection.

The phrase “substantially identical”, in the context of two nucleic acids or polypeptides refers to two or more sequences or subsequences that have at least about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90, about 95%, about 98%, or about 99% or more nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm or by visual inspection. Such “substantially identical” sequences are typically considered to be “homologous” without reference to actual ancestry. Preferably, the “substantial identity” exists over a region of the sequences that is at least about 50 residues in length, more preferably over a region of at least about 100 residues, and most preferably, the sequences are substantially identical over at least about 150 residues, at least about 250 residues, or over the full length of the two sequences to be compared.

Homologs of the acsA gene product include enzymes falling under Enzyme Commission (EC) number 6.2.1.1. Non-limiting examples of homologs of the acsA gene product in various microorganisms include the acetyl-coenzyme A synthetase from Fischerella sp. JSC-11 represented by GenBank Accession No. ZP_(—)08986431.1, the acetyl-coenzyme A from Moorea producta 3L synthetase represented by GenBank Accession No. ZP_(—)08425677.1, the acetate/CoA from Cyanothece sp. PCC 7822 ligase represented by GenBank Accession No. YP_(—)003886065.1, the acetyl-CoA from Cyanothece sp. PCC 7424 synthetase represented by GenBank Accession No. YP_(—)002378472.1, the unnamed protein product from Thermosynechococcus elongatus BP-1 represented by GenBank Accession No. NP_(—)681677.1, the unnamed protein product from Anabaena variabilis ATCC 29413 represented by GenBank Accession No. YP_(—)321725.1, the acetate-CoA ligase from Cylindrospermopsis raciborskii CS-505 represented by GenBank Accession No. ZP_(—)06308209.1, the acetyl-CoA synthetase from Nostoc punctiforme PCC 73102 represented by GenBank Accession No. YP_(—)001869493.1, the acetate-CoA ligase from Microcoleus chthonoplastes PCC 7420 represented by GenBank Accession No. ZP_(—)05030125.1, the acetyl-coenzyme A synthetase from Nodularia spumigena CCY9414 represented by GenBank Accession No. ZP_(—)01629204.1, the acetyl-CoA synthetase from Microcystis aeruginosa NIES-843 represented by GenBank Accession No. YP_(—)001660936.1, the acetate/CoA ligase from ‘Nostoc azollae’ 0708 represented by GenBank Accession No. YP_(—)003723268.1, the acsA gene product from Microcystis aeruginosa PCC 7806 represented by GenBank Accession No. CAO86486.1, the acetyl-coenzyme A synthetase from Microcoleus vaginatus FGP-2 represented by GenBank Accession No. ZP_(—)08490634.1, the Acetate-CoA ligase from Raphidiopsis brookii D9 represented by GenBank Accession No. ZP_(—)06304063.1, the acsA gene product from Acaryochloris marina MBIC11017 represented by GenBank Accession No. YP_(—)001517064.1, the acetyl-CoA synthetase from Acaryochloris sp. CCMEE 5410 represented by GenBank Accession No. ZP_(—)09248274.1, the acetyl-CoA synthetase from Oscillatoria sp. PCC 6506 represented by GenBank Accession No. ZP_(—)07113076.1, the acetyl-CoA synthetase from Cyanothece sp. PCC 7425 represented by GenBank Accession No. YP_(—)002484565.1, the Acetate-CoA ligase from Lyngbya sp. PCC 8106 represented by GenBank Accession No. ZP_(—)01623739.1, the unnamed protein product from Trichodesmium erythraeum IMS101 represented by GenBank Accession No. YP_(—)722064.1, the acetyl-CoA synthetase from Arthrospira platensis str. Paraca represented by GenBank Accession No. ZP_(—)06383883.1, the acetate/CoA ligase from Arthrospira maxima CS-328 represented by GenBank Accession No. ZP_(—)03274675.1, the acetyl-coenzyme A synthetase from Arthrospira sp. PCC 8005 represented by GenBank Accession No. ZP_(—)09782650.1, the acetate/CoA ligase from Arthrospira maxima CS-328 represented by GenBank Accession No. EDZ93724.1, the acetyl-coenzyme A synthetase from Arthrospira sp. PCC 8005 represented by GenBank Accession No. CCE18403.1, the unnamed protein product from Cyanothece sp. PCC 8802 represented by GenBank Accession No. YP_(—)003138301.1, the acetate/CoA ligase from Cyanothece sp. PCC 8802 represented by GenBank Accession No. ACV01466.1, the acetyl-CoA synthetase from Cyanothece sp. PCC 8801 represented by GenBank Accession No. YP_(—)002373634.1, the acetyl-coenzyme A synthetase from Cyanothece sp. ATCC 51472 represented by GenBank Accession No. ZP_(—)08974038.1, the unnamed protein product from Synechococcus elongatus PCC 6301 represented by GenBank Accession No. ZP_(—)08974038.1, the acetyl-CoA synthetase from Cyanothece sp. ATCC 51142 represented by GenBank Accession No. YP_(—)001803432.1, the acetyl-coenzyme A synthetase from Cyanothece sp. CCY0110 represented by GenBank Accession No. ZP_(—)01730332.1, the AMP-dependent synthetase and ligase from Crocosphaera watsonii WH 8501 represented by GenBank Accession No. ZP_(—)00514814.1, the acetate-CoA ligase from Synechococcus sp. PCC 7335 represented by GenBank Accession No. ZP_(—)05036109.1, the acetyl-coenzyme A synthetase from Synechococcus sp. WH 8102 represented by GenBank Accession No. NP_(—)897106.1, the acetate-CoA ligase from Synechococcus sp. WH 7805 represented by GenBank Accession No. ZP_(—)01123920.1, the acetate-CoA ligase from Synechococcus sp. WH 8109 represented by GenBank Accession No. ZP_(—)05788236.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. MIT 9313 represented by GenBank Accession No. NP_(—)894222.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. MIT 9303 represented by GenBank Accession No. YP_(—)001017906.1, the acetyl-CoA synthetase from Synechococcus sp. WH 7803 represented by GenBank Accession No. YP_(—)001224763.1, the acetyl-coenzyme A synthetase from Synechococcus sp. RS9917 represented by GenBank Accession No. ZP_(—)01080065.1, the acetyl-coenzyme A synthetase from Synechococcus sp. WH 8016 represented by GenBank Accession No. ZP_(—)08955323.1, the acetate-CoA ligase from Synechococcus sp. CC9311 represented by GenBank Accession No. YP_(—)730758.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. MIT 9211 represented by GenBank Accession No. YP_(—)001550915.1, the acetate-CoA ligase from Synechococcus sp. CC9902 represented by GenBank Accession No. YP_(—)377326.1, the acetate-CoA ligase from Synechococcus sp. BL107 represented by GenBank Accession No. ZP_(—)01467683.1, the acetyl-coenzyme A synthetase from Synechococcus sp. RS9916 represented by GenBank Accession No. ZP_(—)01471857.1, the acetyl-coenzyme A synthetase from Synechococcus sp. CC9605 represented by GenBank Accession No. YP_(—)381449.1, the acetyl-coenzyme A synthetase from Synechococcus sp. CB0205 represented by GenBank Accession No. ZP_(—)07971118.1, the acetyl-CoA synthetase from Synechococcus sp. RCC307 represented by GenBank Accession No. YP_(—)001227601.1, the acetyl-coenzyme A synthetase from Synechococcus sp. CB0101 represented by GenBank Accession No. ZP_(—)07973216.1, the acetate-CoA ligase from Cyanobium sp. PCC 7001 represented by GenBank Accession No. ZP_(—)05043915.1, the acetate-CoA ligase from Synechococcus sp. WH 5701 represented by GenBank Accession No. ZP_(—)01085120.1, the acs gene product from Prochlorococcus marinus subsp. marinus str. CCMP1375 represented by GenBank Accession No. NP_(—)875433.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. NATL2A represented by GenBank Accession No. YP_(—)291252.1, the acetyl-coenzyme A synthetase from Gloeobacter violaceus PCC 7421 represented by GenBank Accession No. NP_(—)923105.1, the acetyl-coenzyme A synthetase from cyanobacterium UCYN-A represented by GenBank Accession No. YP_(—)003421821.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. NATL1A represented by GenBank Accession No. YP_(—)001014503.1, the acetyl-coenzyme A synthetase from Singulisphaera acidiphila DSM 18658 represented by GenBank Accession No. ZP_(—)09573232.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus subsp. pastoris str. CCMP1986 represented by GenBank Accession No. NP_(—)892737.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. MIT 9312 represented by GenBank Accession No. YP_(—)397116.1, the acetate/CoA ligase from Meiothermus ruber DSM 1279 represented by GenBank Accession No. YP_(—)003507084.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. MIT 9215 represented by GenBank Accession No. YP_(—)001483902.1, the acs gene product from Prochlorococcus marinus str. AS9601 represented by GenBank Accession No. YP_(—)001009068.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. MIT 9515 represented by GenBank Accession No. YP_(—)001011000.1, the acetate-CoA ligase from Prochlorococcus marinus str. MIT 9202 represented by GenBank Accession No. ZP_(—)05137406.1, the acetyl-coenzyme A synthetase from Marinithermus hydrothermalis DSM 14884 represented by GenBank Accession No. YP_(—)004368660.1, the acetyl-coenzyme A synthetase from Prochlorococcus marinus str. MIT 9301 represented by GenBank Accession No. YP_(—)001090869.1, the unnamed protein product from Nostoc sp. PCC 7120 represented by GenBank Accession No. NP_(—)488297.1, the acetate/CoA ligase from Truepera radiovictrix DSM 17093 represented by GenBank Accession No. YP_(—)003703935.1, the acetate/CoA ligase from Haliangium ochraceum DSM 14365 represented by GenBank Accession No. YP_(—)003269915.1, the acetyl-coenzyme A synthetase from Gemmata obscuriglobus UQM 2246 represented by GenBank Accession No. ZP_(—)02733777.1, the acetyl-coenzyme A synthetase from Isosphaera pallida ATCC 43644 represented by GenBank Accession No. YP_(—)004179760.1, the acetyl-CoA synthetase from Chloroherpeton thalassium ATCC 35110 represented by GenBank Accession No. YP_(—)001995147.1, the acetate-CoA ligase from Planctomyces maris DSM 8797 represented by GenBank Accession No. ZP_(—)01856978.1, the acetyl-CoA synthetase from Thermus thermophilus HB8 represented by GenBank Accession No. YP_(—)144514.1, the acetate/CoA ligase from Planctomyces limnophilus DSM 3776 represented by GenBank Accession No. YP_(—)003632128.1, the acetyl-CoA synthetase from Thermus thermophilus HB27 represented by GenBank Accession No. YP_(—)004855.1, the acetyl-coenzyme a synthetase from Oceanithermus profundus DSM 14977 represented by GenBank Accession No. YP_(—)004057553.1, the acetyl-coenzyme A synthetase from Candidatus Koribacter versatilis Ellin345 represented by GenBank Accession No. YP_(—)592595.1, the acetate/CoA ligase from Meiothermus silvanus DSM 9946 represented by GenBank Accession No. YP_(—)003684983.1, the acetate-CoA ligase from Verrucomicrobium spinosum DSM 4136 represented by GenBank Accession No. ZP_(—)02931268.1, the acetate/CoA ligase from Thermus aquaticus Y51MC23 represented by GenBank Accession No. ZP_(—)03496427.1, the acetyl-coenzyme A synthetase from Symbiobacterium thermophilum IAM 14863 represented by GenBank Accession No. YP_(—)074710.1, the acetate/CoA ligase from bacterium Ellin 514 represented by GenBank Accession No. ZP_(—)03630513.1, the acetyl-CoA synthetase from uncultured candidate division OP1 bacterium represented by GenBank Accession No. BAL56248.1, the acetyl-coenzyme A synthetase from Blastopirellula marina DSM 3645 represented by GenBank Accession No. ZP_(—)01092728.1, the acs2 gene product from Thermus scotoductus SA-01 represented by GenBank Accession No. YP_(—)004201921.1, the acetyl-coenzyme A synthetase from Archaeoglobus veneficus SNP6 represented by GenBank Accession No. YP_(—)004341076.1, the Acetyl-coenzyme A synthetase from Desulfitobacterium dehalogenans ATCC 51507 represented by GenBank Accession No. ZP_(—)09634500.1, the unnamed protein product from Candidatus Chloracidobacterium thermophilum B represented by GenBank Accession No. YP_(—)004864177.1, the acetate-CoA ligase from Acidobacterium capsulatum ATCC 51196 represented by GenBank Accession No. YP_(—)002755829.1, the acetate/CoA ligase from Pirellula staleyi DSM 6068 represented by GenBank Accession No. YP_(—)003369860.1, the acetyl-CoA synthetase from Chlorobium chlorochromatii CaD3 represented by GenBank Accession No. YP_(—)379980.1, the acetate-CoA ligase from Myxococcus xanthus DK 1622 represented by GenBank Accession No. YP_(—)630789.1, the acetate-CoA ligase from Myxococcus fulvus HW-1 represented by GenBank Accession No. YP_(—)004667083.1, the unnamed protein product from Candidatus Solibacter usitatus Ellin 6076 represented by GenBank Accession No. YP_(—)829106.1, the acetyl-coenzyme A synthetase from Planctomyces brasiliensis DSM 5305 represented by GenBank Accession No. YP_(—)004268501.1, the acetyl-CoA synthetase from Escherichia coli UMN026 represented by GenBank Accession No. YP_(—)002415210.1, the acetyl-CoA synthetase from Escherichia coli FVEC1412 represented by GenBank Accession No. ZP_(—)06646805.1, the acetyl-coenzyme A synthetase from Escherichia coli FVEC1302 represented by GenBank Accession No. ZP_(—)06988121.1, the acetate-CoA ligase from Escherichia coli MS198-1 represented by GenBank Accession No. ZP_(—)07115900.1, the acetyl-CoA synthetase from Escherichia coli UMN₀₂₆ represented by GenBank Accession No. CAR15720.1, the Acs2p from Saccharomyces cerevisiae S288c represented by GenBank Accession No. NP_(—)013254.1, the acetyl CoA synthetase from Saccharomyces cerevisiae YJM789 represented by GenBank Accession No. EDN59693.1, the K7_Acs2p from Saccharomyces cerevisiae Kyokai no. 7 represented by GenBank Accession No. GAA25035.1, the acetyl CoA synthetase from Saccharomyces cerevisiae RM11-1a represented by GenBank Accession No. EDV09449.1, the bifunctional acetyl-CoA synthetase and propionyl-CoA synthetase from Escherichia coli str. K12 substr. W3110 represented by GenBank Accession No. BAE78071.1, and the acetyl-coenzyme A synthetase from Pseudomonas fulva 12-X represented by GenBank Accession No. YP_(—)004473024.1, among others. The coding sequences encoding these gene products can be found in GenBank (http://www.ncbi.nlm.nih.gov/GenBank/).

Homologs of acsA and AcsA discussed in the examples include the acetyl-CoA synthetase from Synechocystis sp. PCC 6803 (s110542; GenBank Accession No. NP_(—)442428.1; SEQ ID NOS:3 and 4) and the unnamed protein product from Synechococcus sp. PCC 7942 (SYNPCC7942_(—)1342; GenBank Accession No. YP_(—)400369.1; SEQ ID NOS:5 and 6)

The microorganism of the present invention preferably includes any microorganism that harbors an acsA gene or homolog thereof or expresses an acsA gene product or homolog thereof that is capable of being functionally deleted to render the microorganism more tolerant of organic acids. The microorganism may be eukaryotic, such as yeast, or prokaryotic, such as bacteria or archaea. Among bacteria, gram-positive, gram-negative, and ungrouped bacteria are suitable. Phototrophs, lithotrophs, and organotrophs are also suitable. In preferred versions of the invention, the microorganism is a phototroph, such as a cyanobacterium. Suitable cyanobacteria include those from the genuses Agmenellum, Anabaena, Aphanocapsa, Arthrosprira, Gloeocapsa, Haplosiphon, Mastigocladus, Nostoc, Oscillatoria, Prochlorococcus, Scytonema, Synechococcus, and Synechocystis. Preferred cyanobacteria include those selected from the group consisting of Synechococcus spp., spp., Synechocystis spp., and Nostoc spp. Particularly suitable examples of Synechococcus spp. include Synechococcus sp. PCC 7942 and Synechococcus sp. PCC 7002. A particularly suitable example of Synechocystis spp. includes Synechocystis sp. PCC 6803. A benefit of phototrophs is that they require only CO₂ as a carbon source and are not dependent on food-based commodities or other types of biomass for which there is a growing high demand.

Functional deletion of the acsA gene product or homolog thereof in the microorganism results in increased tolerance of the microorganism to organic acids compared to a corresponding microorganism. As used herein, “corresponding microorganism” refers to a microorganism of the same species having the same or substantially same genetic and proteomic composition as a microorganism of the invention, with the exception of genetic and proteomic differences resulting from the modifications described herein for the microorganisms of the invention. Such tolerance is with respect to any organic acid present within the organism or its growth medium, particularly those that may be present in high abundance. Non-limiting examples of organic acids to which the microorganisms of the present invention have increased tolerance include acetic acid, acrylic acid, aspartic acid, benzoic acid, butyric acid, citric acid, formic acid, fumaric acid, furan dicarboxylic acid (2,5-furandicarboxylic acid), glucaric acid, glutamic acid, heptanoic acid, hexanoic acid, 3-hydroxypropionic acid (3HP), isophthalic acid, itaconic acid, lactic acid, levoascorbic acid, levulinic acid, malic acid, octanoic acid, oxalic acid, pentanoic acid, phosphoric acid, propionic acid, pyruvic acid, succinic acid (1,4 succinic acid), and terephthalic acid, among others. The examples show various aspects of increased tolerance to exemplary organic acids 3-hydroxypropionic acid (3HP), acrylic acid, and propionic acid.

One aspect of the increased tolerance to organic acids is an increase in the minimal inhibitory concentration (MIC) of a particular organic acid compared to a corresponding microorganism. MIC is the lowest concentration of an agent that will inhibit growth of a microorganism. An MIC can be determined by titrating the agent in the growth medium of the microorganism. The lowest concentration of the agent in which the microorganism is no longer able to grow is the MIC. Methods of culturing microorganisms and of detecting their growth are well known in the art and are not discussed in detail herein. A relative increase in MIC indicates a higher tolerance to an agent and indicates that the microorganism can grow in the presence of a higher concentration of the agent. Conversely, a relative decrease in MIC indicates a lower tolerance to an agent and indicates that the microorganism can grow only in the presence of a lower concentration of the agent.

Functional deletion of the acsA gene product or homolog thereof in the microorganism confers an MIC of at least about 10 μM, 25 μM, 50 μM, 75 μM, 100 μM, 250 μM, 500 μM, 1 mM, 25 mM, 50 mM, 70 mM, 100 mM, 125 mM, or 150 mM to acrylic acid; an MIC of at least about 10 mM, 15 mM, 20 mM, 25 mM, 50 mM, 75 mM, 100 mM, 125 mM, 150 mM, 175 mM, 200 mM, 225 mM, 250 mM, 260 mM, 300 mM, 350 mM, or more to 3HP; and/or an MIC of at least about 250 μM, 500 μM, 1 mM, 50 mM, 100 mM, 200 mM, 300 mM, 350 mM, 400 mM, 450 mM, 500 mM, or more to propionic acid. Such MICs occur in at least Synechococcus sp. cyanobacteria, such as Synechococcus sp. PCC 7002 and Synechococcus sp. PCC 7942, when assayed at a pH of about 8. Such MICs also occur in Synechocystis sp., such as Synechocystis sp. PCC 6803, when assayed at a pH of about 8. Such MICs also occur in any other microorganism described herein, such as Prochlorococcus sp., Nostoc sp., or others.

Another aspect of increased tolerance is increased growth rate in the presence of a certain concentration of an organic acid or an equal growth rate in the presence of an increased concentration of an organic acid compared to a corresponding microorganism.

In various aspects of the invention, functional deletion of the acsA gene product or homolog thereof in the microorganism confers at least about a 1.5-fold, a 5-fold, a 10-fold, a 15-fold, a 25-fold, a 50-fold, a 75-fold, a 100-fold, a 500-fold, a 750-fold, a 1.000-fold, 1.250-fold, a 1.500-fold, a 1.750-fold, a 2.000-fold, a 2.250-fold, a 2.500-fold, a 2.750-fold, a 3.000-fold, a 3.250-fold, or a 3.500-fold increase in tolerance against an organic acid. The organic acid to which functional deletion of the acsA gene product confers such MICs may include acrylic acid, 3HP, propionic acid, or lactic acid, among others. In some versions of the invention, for example, functional deletion of the acsA gene product in Synechococcus sp. PCC 7002 confers at least about a 2.800-fold increase in MIC for acrylic acid, at least about a 26-fold increase in MIC for 3HP, and at least about a 100-fold increase in MIC for propionic acid at pH of about 8 (see examples below).

The increased tolerance to organic acids conferred by functional deletion of the acsA gene product or homolog thereof renders the microorganism particularly suited for producing high amounts of organic acids, many of which have industrial utility. Accordingly, the microorganism in some versions of the invention is capable of producing an organic acid that can be isolated for industrial purposes. The microorganism may be able to naturally make the organic acid, may be genetically modified to make the organic acid, or may be genetically modified to make increased amounts of the organic acid that it already makes. Non-limiting examples of organic acids that the microorganisms of the present invention can produce include acetic acid, aspartic acid, benzoic acid, citric acid, formic acid, fumaric acid, furan dicarboxylic acid (2,5-furandicarboxylic acid), glucaric acid, glutamic acid, 3-hydroxypropionic acid (3HP), isophthalic acid, itaconic acid, lactic acid, levoascorbic acid, levulinic acid, malic acid, oxalic acid, phosphoric acid, propionic acid, pyruvic acid, succinic acid (1,4 succinic acid), and terephthalic acid, among others. In preferred versions of the invention, the microorganism is capable of making at least 3HP and or lactic acid.

The microorganism may be modified to express or increase expression of one or more genes involved in the production of the organic acid. Modifying the microorganism to express or increase expression of a gene can be performed using any methods currently known in the art or discovered in the future. Examples include genetically modifying the microorganism and culturing the microorganism in the presence of factors that increase expression of the gene. Suitable methods for genetic modification include but are not limited to placing the coding sequence under the control of a more active promoter, increasing the copy number of the gene, and/or introducing a translational enhancer on the gene (see, e.g., Olins et al. Journal of Biological Chemistry, 1989, 264(29):16973-16976). Increasing the copy number of the gene can be performed by introducing additional copies of the gene to the microorganism, i.e., by incorporating one or more exogenous copies of the native gene or a heterologous homolog thereof into the microbial genome, by introducing such copies to the microorganism on a plasmid or other vector, or by other means. “Exogenous” used in reference to a genetic element means the genetic element is introduced to a microorganism by genetic modification. “Heterologous” used in reference to a genetic element means that the genetic element is derived from a different species. A promoter that controls a particular coding sequence is herein described as being “operationally connected” to the coding sequence.

The microorganisms of the invention may include at least one recombinant nucleic acid configured to express or overexpress a particular enzyme. “Recombinant” as used herein with reference to a nucleic acid molecule or polypeptide is one that has a sequence that is not naturally occurring, has a sequence that is made by an artificial combination of two otherwise separated segments of sequence, or both. This artificial combination can be achieved, for example, by chemical synthesis or by the artificial manipulation of isolated segments of nucleic acid molecules or polypeptides, such as genetic engineering techniques. “Recombinant” is also used to describe nucleic acid molecules that have been artificially modified but contain the same regulatory sequences and coding regions that are found in the organism from which the nucleic acid was isolated. A recombinant cell or microorganism is one that contains a recombinant nucleic acid molecule or polypeptide. “Overexpress” as used herein means that a particular gene product is produced at a higher level in one cell, such as a recombinant cell, than in a corresponding cell. For example, a microorganism that includes a recombinant nucleic acid configured to overexpress an enzyme produces the enzyme at a greater amount than a microorganism that does not include the recombinant nucleic acid.

In some versions of the invention, the microorganism is genetically modified to produce or enhance production of 3HP. Such a microorganism can be obtained by expressing or increasing expression of a gene for any one or more of the enzymes catalyzing the various steps in a 3HP-production pathway. Non-limiting examples of suitable enzymes include pyruvate kinase, pyruvate dehydrogenase, acetyl-CoA carboxylase, malonyl-CoA reductase, malonate semialdehyde reductase, phosphoenolpyruvate carboxylase, aspartate aminotransferase, aspartate decarboxylase, and β-alanine/α-ketoglutarate aminotransferase. See FIGS. 7, 9A, and 9B. See also U.S. Pat. No. 8,048,624 to Lynch, U.S. Pub. 2011/0125118 to Lynch, U.S. Pub. 2010/0210017 to Gill et al., and Warnecke et al. Metabolic Engineering (2010) 12:241-250 for additional enzymes.

Accordingly, some microorganisms of the invention include at least one recombinant nucleic acid configured to express or overexpress a malonyl-CoA reductase. Malonyl-CoA reductases include the enzymes classified under EC 1.2.1.75. In some versions, the microorganism is modified to harbor a nucleic acid encoding the malonyl-CoA reductase from Chloroflexus aurantiacus or a homolog thereof. The coding sequence for the malonyl-CoA reductase from Chloroflexus aurantiacus is included in GenBank under accession number AY530019 and is represented by SEQ ID NO:7. The Chloroflexus aurantiacus malonyl-CoA reductase gene product is included in GenBank under accession number AAS20429 and has an amino acid sequence represented by SEQ ID NO:8. The malonyl-CoA reductase from Chloroflexus aurantiacus has been shown to be a bi-functional enzyme, having activity that converts malonyl-CoA to malonate semialdehyde in addition to activity that converts malonate semialdehyde to 3HP.

Exemplary homologs of the Chloroflexus aurantiacus malonyl-CoA reductase gene product include but are not limited to the short-chain dehydrogenase/reductase SDR from Chloroflexus aggregans DSM 9485 represented by GenBank Accession No. YP_(—)002462600.1, the short-chain dehydrogenase/reductase SDR from Oscillochloris trichoides DG6 represented by GenBank Accession No. ZP_(—)07684596.1, the short-chain dehydrogenase/reductase SDR from Roseiflexus castenholzii DSM 13941 represented by GenBank Accession No. YP_(—)001433009.1, the short-chain dehydrogenase/reductase SDR from Roseiflexus sp. RS-1 represented by GenBank Accession No. YP_(—)001277512.1, among others. The coding sequences encoding these gene products can be found in GenBank.

Homologs of the Chloroflexus aurantiacus malonyl-CoA reductase also include enzymes having an amino acid sequence at least about 80%, 85%, 90%, 95%, 97%, 98%, 99% or more identical to SEQ ID NO:8. Sequences having these percent identities can be obtained by aligning SEQ ID NO:8 to the sequences of the Chloroflexus aurantiacus malonyl-CoA reductase homologs listed above or otherwise known in the art to determine which residues are amenable to variation (i.e., substitution, deletion, addition, etc.) and the identities of the suitably substituted or added residues.

In some versions of the invention, the microorganism is modified to harbor a nucleic acid encoding the malonyl-CoA reductase from Sulfolobus tokodaii or a homolog thereof. The coding sequence for the malonyl-CoA reductase from Sulfolobus tokodaii is included in GenBank under accession number NC_(—)003106.2 (positions 2170729-2171808; Gene ID 1460244) and is represented by SEQ ID NO:11. A truncated, codon-optimized version of the coding sequence preferred for expression in cyanobacteria is represented by SEQ ID NO:12. The gene product of the malonyl-CoA reductase from Sulfolobus tokodaii is included in GenBank under accession number NP_(—)378167. A truncated gene product encoded by SEQ ID NO:12 and suitable for use in the present invention has an amino acid sequence represented by SEQ ID NO:13. The malonyl-CoA reductase from Sulfolobus tokodaii has been shown to have activity that converts malonyl-CoA to malonate semialdehyde. It does not appear to have activity that converts malonate semialdehyde to 3HP.

Exemplary homologs of the malonyl-CoA reductase from Sulfolobus tokodaii include but are not limited to the aspartate-semialdehyde dehydrogenase from Acidianus hospitalis W1 represented by GenBank Accession No. YP_(—)004459517.1, the aspartate-semialdehyde dehydrogenase from Metallosphaera sedula DSM 5348 represented by GenBank Accession No. YP_(—)001190808.1, the malonyl-/succinyl-CoA reductase from Metallosphaera cuprina Ar-4 represented by GenBank Accession No. YP_(—)004410014.1, the aspartate-semialdehyde dehydrogenase from Sulfolobales archaeon AZ1 represented by GenBank Accession No. EWG07552.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus solfataricus P2 represented by GenBank Accession No. NP_(—)343563.1, the aspartate-semialdehyde dehydrogenase from Metallosphaera yellowstonensis represented by GenBank Accession No. WP_(—)009071519.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus islandicus M.16.27 represented by GenBank Accession No. YP_(—)002844727.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus islandicus L.S.2.15 represented by GenBank Accession No. YP_(—)002833533.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus islandicus HVE10/4 represented by GenBank Accession No. YP_(—)005647305.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus islandicus Y.N.15.51 represented by GenBank Accession No. YP_(—)002841967.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus acidocaldarius DSM 639 represented by GenBank Accession No. YP_(—)256941.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus islandicus M.14.25 represented by GenBank Accession No. YP_(—)002830795.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus acidocaldarius SUSAZ represented by GenBank Accession No. YP_(—)008948306.1, the aspartate-semialdehyde dehydrogenase from Sulfolobales archaeon Acd1 represented by GenBank Accession No. WP_(—)020198954.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus acidocaldarius DSM 639 represented by GenBank Accession No. YP_(—)256733.1, the aspartate-semialdehyde dehydrogenase from Sulfolobus acidocaldarius SUSAZ represented by GenBank Accession No. YP_(—)008948046.1, the aspartate-semialdehyde dehydrogenase from Archaeoglobus profundus DSM 5631 represented by GenBank Accession No. YP_(—)003401535.1, the aspartate-semialdehyde dehydrogenase from Candidatus Caldiarchaeum subterraneum represented by GenBank Accession No. YP_(—)008797381.1, the aspartate-semialdehyde dehydrogenase from Ferroglobus placidus DSM 10642 represented by GenBank Accession No. YP_(—)003435562.1, the aspartate-semialdehyde dehydrogenase from Methanothermobacter marburgensis str. Marburg represented by GenBank Accession No. YP_(—)003850098.1, the aspartate-semialdehyde dehydrogenase from Methanothermobacter thermautotrophicus CaT2 represented by GenBank Accession No. BAM69964.1, the aspartate-semialdehyde dehydrogenase from Methanothermobacter thermautotrophicus str. Delta H represented by GenBank Accession No. NP_(—)275938.1, the aspartate semialdehyde dehydrogenase from Archaeoglobus sulfaticallidus PM70-1 represented by GenBank Accession No. YP_(—)007906903.1, the aspartate-semialdehyde dehydrogenase from Pyrobaculum arsenaticum DSM 13514 represented by GenBank Accession No. YP_(—)001153189.1, the aspartate semialdehyde dehydrogenase from Methanothermus fervidus DSM 2088 represented by GenBank Accession No. YP_(—)004004235.1, and the aspartate-semialdehyde dehydrogenase from Methanopyrus kandleri AV19 represented by GenBank Accession No. NP_(—)614672.1, among others. The coding sequences encoding these gene products can be found in GenBank.

Homologs of the Sulfolobus tokodaii malonyl-CoA reductase also include enzymes having an amino acid sequence at least about 80%, 85%, 90%, 95%, 97%, 98%, 99% or more identical to SEQ ID NO:13. Sequences having these percent identities can be obtained by aligning SEQ ID NO:13 to the sequences of the Sulfolobus tokodaii malonyl-CoA reductase homologs listed above or otherwise known in the art to determine which residues are amenable to variation (i.e., substitution, deletion, addition, etc.) and the identities of the suitably substituted or added residues.

In some versions of the invention, the microorganism is modified to express or increase expression of a malonate semialdehyde reductase. Malonate semialdehyde reductase converts malonate semialdehyde to 3HP. Such a modification is preferred in microorganisms modified to express or increase expression of a malonyl-CoA reductase that does not convert malonate semialdehyde to 3HP, such as the malonyl-CoA reductase from Sulfolobus tokodaii. Suitable malonate semialdehyde reductases can use either NADH (EC 1.1.1.59) or NADPH (EC 1.1.1.298) as cofactors. Malonate semialdehyde reductases that use NADPH are preferred. In some versions, the microorganism is modified to harbor a nucleic acid encoding the malonate semialdehyde reductase from Metallosphaera sedula or a homolog thereof. The coding sequence of the malonate semialdehyde reductase from Metallosphaera sedula is included in GenBank under accession number NC_(—)009440.1 (Gene ID 5103380; positions 1929295-1930239) and is represented by SEQ ID NO:14. A codon-optimized version of the coding sequence preferred for expression in cyanobacteria is represented by SEQ ID NO:15. The gene product of the malonate semialdehyde reductase from Metallosphaera sedula is included in GenBank under accession number YP_(—)001192057 and has an amino acid sequence represented by SEQ ID NO:16.

Exemplary homologs of the malonate semialdehyde reductase from Metallosphaera sedula include but are not limited to the 3-hydroxyacyl-CoA dehydrogenase from Metallosphaera sedula DSM 5348 represented by GenBank Accession No. YP_(—)001192057.1, the malonate semialdehyde reductase from Metallosphaera cuprina Ar-4 represented by GenBank Accession No. YP_(—)004408885.1, the 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein from Acidianus hospitalis W1 represented by GenBank Accession No. YP_(—)004458285.1, the 3-hydroxyacyl-CoA dehydrogenase from Sulfolobales archaeon AZ1 represented by GenBank Accession No. EWG08084.1, the 3-hydroxyacyl-CoA dehydrogenase from Metallosphaera yellowstonensis represented by GenBank Accession No. WP_(—)009075415.1, the 3-hydroxyacyl-CoA dehydrogenase from Sulfolobus solfataricus P2 represented by GenBank Accession No. NP_(—)342162.1, the 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein from Sulfolobus islandicus HVE10/4 represented by GenBank Accession No. YP_(—)005646018.1, the 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein from Sulfolobus islandicus REY15A represented by GenBank Accession No. YP_(—)005648646.1, the 3-hydroxyacyl-CoA dehydrogenase from Sulfolobus islandicus LAL14/1 represented by GenBank Accession No. YP_(—)007865821.1, the 3-hydroxyacyl-CoA dehydrogenase from Sulfolobus islandicus M.14.25 represented by GenBank Accession No. YP_(—)002829538.1, the 3-hydroxyacyl-CoA dehydrogenase from Sulfolobus islandicus represented by GenBank Accession No. WP_(—)016732252.1, the 3-hydroxyacyl-CoA dehydrogenase from Sulfolobales archaeon Acd1 represented by GenBank Accession No. WP_(—)020199213.1, the 3-hydroxybutyryl-CoA dehydrogenase from Sulfolobus tokodaii str. 7 represented by GenBank Accession No. NP_(—)377470.1, the 3-hydroxyacyl-CoA dehydrogenase from Sulfolobus acidocaldarius SUSAZ represented by GenBank Accession No. YP_(—)008947634.1, the 3-hydroxybutyryl-CoA dehydrogenase from Sulfolobus acidocaldarius DSM 639 represented by GenBank Accession No. YP_(—)256228.1, the 3-hydroxyacyl-CoA dehydrogenase from Archaeoglobus fulgidus DSM 4304 represented by GenBank Accession No. NP_(—)070034.1, the 3-hydroxyacyl-CoA dehydrogenase from Burkholderia sp. H160 represented by GenBank Accession No. WP_(—)008917830.1, the 3-hydroxyacyl-CoA dehydrogenase represented by hbd-8 from Planctomyces maxis represented by GenBank Accession No. WP_(—)002645585.1, the 3-hydroxybutyryl-CoA dehydrogenase from Megasphaera sp. UPII 199-6 represented by GenBank Accession No. WP_(—)007391670.1, the 3-hydroxyacyl-CoA dehydrogenase from Burkholderia pseudomallei 1026b represented by GenBank Accession No. YP_(—)006275221.1, the 3-hydroxyacyl-CoA dehydrogenase from Burkholderia oklahomensis represented by GenBank Accession No. WP_(—)010114811.1, and the 3-hydroxyacyl-CoA dehydrogenase from Burkholderia pseudomallei MSHR305 represented by GenBank Accession No. YP_(—)008340862.1, among others. The coding sequences encoding these gene products can be found in GenBank.

Homologs of the Metallosphaera sedula malonate semialdehyde reductase also include enzymes having an amino acid sequence at least about 80%, 85%, 90%, 95%, 97%, 98%, 99% or more identical to SEQ ID NO:16. Sequences having these percent identities can be obtained by aligning SEQ ID NO:16 to the sequences of the Metallosphaera sedula malonate semialdehyde reductase homologs listed above or otherwise known in the art to determine which residues are amenable to variation (i.e., substitution, deletion, addition, etc.) and the identities of the suitably substituted or added residues.

In some versions of the invention, the microorganism is modified to express or increase expression of acetyl-CoA carboxylase, either alone, with a malonyl-CoA reductase, with a malonate semialdehyde reductase, or with other enzymes. Such a microorganism can be obtained by introducing exogenous nucleic acids expressing the acetyl-CoA carboxylase subunits into the microorganism, by introducing highly expressed promoters in front of the endogenous acetyl-CoA carboxylase subunit coding sequences, by increasing translational efficiency, or by other means. In bacteria, acetyl-CoA carboxylase is a multisubunit enzyme that is encoded by four genes, accA, accB, accC, and accD. Exemplary acetyl-coA carboxylase subunit genes for use in the present invention can be those found in Synechococcus sp. PCC 7002 or homologs thereof. The complete genome of Synechococcus sp. PCC 7002 can be found in GenBank under Accession No. NC_(—)010475. The coding sequence for accA can be found at positions 2536162-2537139 of NC_(—)010475, the gene product of which has a sequence represented by GenBank Accession No. YP_(—)001735676.1. The coding sequence for accB can be found at positions 60707-61204 of NC_(—)010475, the gene product of which has a sequence represented by GenBank Accession No. YP_(—)001733325.1. The coding sequence for accC can be found at positions 2210473-2211819 of NC_(—)010475, the gene product of which has a sequence represented by GenBank Accession No. YP_(—)001735364.1″. The coding sequence for accD can be found at positions 64484-65443 of NC_(—)010475, the gene product of which has a sequence represented by GenBank Accession No. YP_(—)001733331.1. Suitable promoters for increasing expression of these genes are known in the art. In some versions of the invention, an artificial operon comprising the accD, accA, accB, and accC coding sequences from E. coli can be introduced into the microorganism for expression or overexpression of acetyl-CoA carboxylase. See, e.g., US 2011/0165637 to Pfleger et al., which is incorporated herein by reference.

In some versions of the invention, the microorganism is genetically modified to produce or enhance production of lactate. Such a microorganism can be obtained by expressing or increasing expression of lactate dehydrogenase. Lactate dehydrogenase catalyzes the conversion of pyruvate to lactate. See FIG. 12A. Lactate dehydrogenases include the enzymes classified under EC 1.1.1.27 (L-lactate dehydrogenases) and 1.1.1.28 (D-lactate dehydrogenases). L-Lactate dehydrogenases are preferred.

In some versions of the invention, the microorganism is modified to harbor a nucleic acid encoding a lactate dehydrogenase from Bacillus subtilis or a homolog thereof. The coding sequence of the lactate dehydrogenase from Bacillus subtilis is included in GenBank under accession number AL009126.3 (positions 329774 to 330739) and is represented by SEQ ID NO:17. The gene product of the lactate dehydrogenase from Bacillus subtilis is included in GenBank under accession number NP_(—)388187 and has an amino acid sequence represented by SEQ ID NO:18.

Exemplary homologs of the lactate dehydrogenase from Bacillus subtilis include but are not limited to the L-lactate dehydrogenase from Bacillus subtilis subsp. subtilis str. 168 represented by GenBank Accession No. NP_(—)388187.2, the L-lactate dehydrogenase from Bacillus subtilis subsp. natto BEST195 represented by GenBank Accession No. YP_(—)005559471.1, the L-lactate dehydrogenase from Bacillus subtilis BSn5 represented by GenBank Accession No. YP_(—)004206262.1, the L-lactate dehydrogenase from Bacillus subtilis subsp. spizizenii TU-B-10 represented by GenBank Accession No. YP_(—)004875853.1, the lactate dehydrogenase from Bacillus subtilis represented by GenBank Accession No. WP_(—)017696103.1, the lactate dehydrogenase from Bacillus subtilis represented by GenBank Accession No. WP_(—)003224788.1, the L-lactate dehydrogenase from Bacillus subtilis subsp. subtilis str. RO-NN-1 represented by GenBank Accession No. YP_(—)005555343.1, the L-lactate dehydrogenase from Bacillus subtilis XF-1 represented by GenBank Accession No. YP_(—)007425489.1, the L-lactate dehydrogenase from Bacillus subtilis represented by GenBank Accession No. WP_(—)003241205.1, the lactate dehydrogenase from Bacillus subtilis represented by GenBank Accession No. WP_(—)019257406.1, the lactate dehydrogenase from Bacillus mojavensis represented by GenBank Accession No. WP_(—)010332943.1, the lactate dehydrogenase from Bacillus vallismortis represented by GenBank Accession No. WP_(—)010331365.1, the L-lactate dehydrogenase from Bacillus subtilis subsp. spizizenii str. W23 represented by GenBank Accession No. YP_(—)003864678.1, the L-lactate dehydrogenase from Bacillus atrophaeus represented by GenBank Accession No. WP_(—)010787568.1, the lactate dehydrogenase from Bacillus amyloliquefaciens LFB112 represented by GenBank Accession No. YP_(—)008948730.1, the L-lactate dehydrogenase from Bacillus licheniformis 9945A represented by GenBank Accession No. YP_(—)008076533.1, the L-lactate dehydrogenase from Halobacillus halophilus DSM 2266 represented by GenBank Accession No. YP_(—)006181877.1, L-lactate dehydrogenase from Halobacillus sp. BAB-2008 represented by GenBank Accession No. WP_(—)008633175.1, the L-lactate dehydrogenase from Geobacillus sp. WCH70 represented by GenBank Accession No. YP_(—)002948666.1, the lactate dehydrogenase from Geobacillus caldoxylosilyticus represented by GenBank Accession No. WP _(—)017436539.1, the L-lactate dehydrogenase from Anoxybacillus flavithermus represented by GenBank Accession No. WP_(—)003394005.1, the lactate dehydrogenase from Anoxybacillus kamchatkensis represented by GenBank Accession No. WP_(—)019416922.1, and the lactate dehydrogenase from Lactococcus lactis represented by GenBank Accession No. NP_(—)267487, among others. The coding sequences encoding these gene products can be found in GenBank.

Homologs of the Bacillus subtilis lactate dehydrogenase also include enzymes having an amino acid sequence at least about 80%, 85%, 90%, 95%, 97%, 98%, 99% or more identical to SEQ ID NO:18. Sequences having these percent identities can be obtained by aligning SEQ ID NO:18 to the sequences of the Bacillus subtilis lactate dehydrogenase homologs listed above or otherwise known in the art to determine which residues are amenable to variation (i.e., substitution, deletion, addition, etc.) and the identities of the suitably substituted or added residues.

In some versions, the microorganism is modified to harbor a nucleic acid encoding the lactate dehydrogenase from Lactococcus lactis or a homolog thereof. The coding sequence of the lactate dehydrogenase from Lactococcus lactis is included in GenBank under accession number NC_(—)002662.1 (Gene ID 1114981, complement of positions 1369224-1370201). A codon-optimized version of the coding sequence preferred for expression in cyanobacteria is represented by SEQ ID NO:21. The gene product of the lactate dehydrogenase from Lactococcus lactis is included in GenBank under accession number NP_(—)267487 and has an amino acid sequence represented by SEQ ID NO:22.

Exemplary homologs of the lactate dehydrogenase from Lactococcus lactis include but are not limited to the L-lactate dehydrogenase from Lactococcus lactis subsp. cremoris UC509.9 represented by GenBank Accession No. YP_(—)006999682.1, the lactate dehydrogenase from Lactococcus lactis represented by GenBank Accession No. WP_(—)021165426.1, the L-lactate dehydrogenase from Lactococcus lactis represented by GenBank Accession No. AAB51677.1, the L-lactate dehydrogenase from Lactococcus lactis represented by GenBank Accession No. AAB51679.1, lactate dehydrogenase from Lactococcus lactis represented by GenBank Accession No. AAA25172.1, the lactate dehydrogenase from Lactococcus lactis subsp. cremoris TIFN6 represented by GenBank Accession No. EQC54698.1, the L-lactate dehydrogenase from Streptococcus anginosus C238 represented by GenBank Accession No. YP_(—)008500777.1, the lactate dehydrogenase from Streptococcus anginosus represented by GenBank Accession No. WP_(—)003029659.1, the lactate dehydrogenase from Lactococcus garvieae represented by GenBank Accession No. WP_(—)003135756.1, the lactate dehydrogenase from Streptococcus anginosus represented by GenBank Accession No. WP_(—)003042963.1, the malate/lactate dehydrogenases from Streptococcus anginosus represented by GenBank Accession No. WP_(—)022525868.1, the L-lactate dehydrogenase from Streptococcus intermedius C270 represented by GenBank Accession No. YP_(—)008497003.1, the L-lactate dehydrogenase from Lactococcus garvieae ATCC 49156 represented by GenBank Accession No. YP_(—)004779491.1, the lactate dehydrogenase from Lactococcus garvieae represented by GenBank Accession No. WP_(—)019293709.1, the L-lactate dehydrogenase from Streptococcus uberis 0140J represented by GenBank Accession No. YP_(—)002562208.1, the L-lactate dehydrogenase from Streptococcus parauberis KCTC 11537 represented by GenBank Accession No. YP_(—)004478812.1, the L-lactate dehydrogenase from Streptococcus intermedius B196 represented by GenBank Accession No. YP_(—)008512752.1, the lactate dehydrogenase from Streptococcus pseudoporcinus represented by GenBank Accession No. WP_(—)007891460.1, the L-lactate dehydrogenase from Streptococcus iniae SF1 represented by GenBank Accession No. YP_(—)008056778.1, the L-lactate dehydrogenase from Streptococcus intermedius JTH08 represented by GenBank Accession No. YP_(—)006469731.1, the lactate dehydrogenase from Streptococcus anginosus represented by GenBank Accession No. WP_(—)003069027.1, the lactate dehydrogenase from Streptococcus porcinus represented by GenBank Accession No. WP_(—)003084658.1, the lactate dehydrogenase from Streptococcus didelphis represented by GenBank Accession No. WP_(—)018365941.1, the L-lactate dehydrogenase from Streptococcus pyogenes M1 GAS represented by GenBank Accession No. NP_(—)269302.1, the L-lactate dehydrogenase from Streptococcus constellatus subsp. pharyngis C1050 represented by GenBank Accession No. YP_(—)008498899.1, the L-lactate dehydrogenase from Streptococcus constellatus subsp. pharyngis C232 represented by GenBank Accession No. YP_(—)008495295.1, the L-lactate dehydrogenase from Streptococcus equi subsp. zooepidemicus MGCS10565 represented by GenBank Accession No. YP_(—)002123389.1, the L-lactate dehydrogenase from Streptococcus dysgalactiae subsp. equisimilis GGS_(—)124 represented by GenBank Accession No. YP_(—)002996624.1, the L-lactate dehydrogenase from Streptococcus equi subsp. equi 4047 represented by GenBank Accession No. YP_(—)002746472.1, the lactate dehydrogenase from Streptococcus marimammalium represented by GenBank Accession No. WP_(—)018369606.1, the lactate dehydrogenase from Streptococcus canis represented by GenBank Accession No. WP_(—)003048552.1, the lactate dehydrogenase from Lactococcus raffinolactis represented by GenBank Accession No. WP_(—)003140351.1, the lactate dehydrogenase from Streptococcus ictaluri represented by GenBank Accession No. WP_(—)008089442.1, the lactate dehydrogenase from Streptococcus iniae represented by GenBank Accession No. WP_(—)017794816.1, the lactate dehydrogenase from Streptococcus merionis represented by GenBank Accession No. WP_(—)018372720.1, the L-lactate dehydrogenase from Streptococcus dysgalactiae subsp. equisimilis 167 represented by GenBank Accession No. YP_(—)008629609.1, and the lactate dehydrogenase from Bacillus subtilis represented by GenBank Accession No. NP_(—)388187, among others. The coding sequences encoding these gene products can be found in GenBank.

Homologs of the Lactococcus lactis lactate dehydrogenase also include enzymes having an amino acid sequence at least about 80%, 85%, 90%, 95%, 97%, 98%, 99% or more identical to SEQ ID NO:22. Sequences having these percent identities can be obtained by aligning SEQ ID NO:22 to the sequences of the Lactococcus lactis lactate dehydrogenase homologs listed above or otherwise known in the art to determine which residues are amenable to variation (i.e., substitution, deletion, addition, etc.) and the identities of the suitably substituted or added residues.

In some versions of the invention, the microorganism is modified to express or increase expression of a transhydrogenase. Preferred transhydrogenases are pyridine nucleotide transhydrogenases, including the enzymes classified under EC 1.6.1.1, 1.6.1.2, and 1.6.1.3. Pyridine nucleotide transhydrogenases convert NAD and NADPH to and from NADH and NADP⁺. See FIG. 12B. Soluble (as opposed to membrane-bound) pyridine nucleotide transhydrogenases are preferred. Other transhydrogenases that produce either NADH or NADPH as a byproduct are also acceptable. Modifying a microorganism to express or increase expression of a transhydrogenase is preferred when the microorganism is modified to express or increase expression of a lactate dehydrogenase. In some versions, the microorganism is modified to harbor a nucleic acid encoding the soluble pyridine nucleotide transhydrogenase from E. coli (particularly E. coli K12 MG1655) or a homolog thereof. The coding sequence of the soluble pyridine nucleotide transhydrogenase from E. coli K12 MG1655 is included in GenBank under accession number U00096.3 (positions 4159390 to 4160790) and is represented by SEQ ID NO:19. The gene product of the soluble pyridine nucleotide transhydrogenase from E. coli K12 MG1655 is included in GenBank under accession number NP_(—)418397 and is represented by SEQ ID NO:20.

Exemplary homologs of the soluble pyridine nucleotide transhydrogenase from E. coli K12 MG1655 include but are not limited to the soluble pyridine nucleotide transhydrogenase from Escherichia coli HS represented by GenBank Accession No. YP_(—)001460757.1, the pyridine nucleotide-disulfide oxidoreductase family protein from Escherichia coli represented by GenBank Accession No. WP_(—)001705589.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)001120797.1, the pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)024228022.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)001120803.1, the soluble pyridine nucleotide transhydrogenase from Shigella flexneri 2a str. 2457T represented by GenBank Accession No. NP_(—)838918.2, the soluble pyridine nucleotide transhydrogenase from Escherichia coli CFT073 represented by GenBank Accession No. NP_(—)756777.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)023278586.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)021576626.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)021541750.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)001403311.1, the soluble pyridine nucleotide transhydrogenase Escherichia coli represented by GenBank Accession No. WP_(—)001120823.1, soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)001120830.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)021549795.1, the pyridine nucleotide-disulfide oxidoreductase family protein from Escherichia coli represented by GenBank Accession No. WP_(—)001385008.1, soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)001120811.1, the soluble pyridine nucleotide transhydrogenase Escherichia coli 536 represented by GenBank Accession No. YP_(—)672034.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)001120808.1, the soluble pyridine nucleotide transhydrogenase from Shigella boydii Sb227 represented by GenBank Accession No. YP_(—)410260.2, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)021539635.1, the pyridine nucleotide-disulfide oxidoreductase family protein from Escherichia coli represented by GenBank Accession No. WP_(—)001546140.1, the soluble pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)001545096.1, the soluble pyridine nucleotide transhydrogenase from Shigella sonnei Ss046 represented by GenBank Accession No. YP_(—)312883.2, the pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)024197343.1, the pyridine nucleotide transhydrogenase from Escherichia coli represented by GenBank Accession No. WP_(—)024172841.1, the pyridine nucleotide-disulfide oxidoreductase family protein from Escherichia coli represented by GenBank Accession No. WP_(—)001646069.1, the pyridine nucleotide-disulfide oxidoreductase family protein from Escherichia coli represented by GenBank Accession No. WP_(—)001561736.1, the pyridine nucleotide-disulfide oxidoreductase family protein from Escherichia coli represented by GenBank Accession No. WP_(—)001406381.1, the soluble pyridine nucleotide transhydrogenase from Shigella flexneri represented by GenBank Accession No. WP_(—)001120814.1, the soluble pyridine nucleotide transhydrogenase from Shigella flexneri represented by GenBank Accession No. WP_(—)001120826.1, the soluble pyridine nucleotide transhydrogenase from Shigella flexneri 1235-66 represented by GenBank Accession No. EIQ63659.1, the soluble pyridine nucleotide transhydrogenase from Escherichia albertii represented by GenBank Accession No. WP_(—)001120820.1, the soluble pyridine nucleotide transhydrogenase from Shigella flexneri represented by GenBank Accession No. WP_(—)001120827.1, the soluble pyridine nucleotide transhydrogenase from Shigella dysenteriae Sd197 represented by GenBank Accession No. YP_(—)405233.2, the soluble pyridine nucleotide transhydrogenase from Salmonella enterica represented by GenBank Accession No. WP_(—)001120792.1, the soluble pyridine nucleotide transhydrogenase from Citrobacter rodentium ICC168 represented by GenBank Accession No. YP_(—)003367222.1, the soluble pyridine nucleotide transhydrogenase from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 represented by GenBank Accession No. YP_(—)219002.1, the soluble pyridine nucleotide transhydrogenase from Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 represented by GenBank Accession No. YP_(—)002048124.1, the soluble pyridine nucleotide transhydrogenase from Enterobacter cloacae subsp. dissolvens SDM represented by GenBank Accession No. YP_(—)006479868.1, the soluble pyridine nucleotide transhydrogenase from Citrobacter represented by GenBank Accession No. WP_(—)016155291.1, the soluble pyridine nucleotide transhydrogenase from Shigella flexneri 1235-66 represented by GenBank Accession No. EIQ78768.1, and the pyridine nucleotide transhydrogenase from Enterobacter asburiae LF7a represented by GenBank Accession No. YP_(—)004830801.1, among others. The coding sequences encoding these gene products can be found in GenBank.

Homologs of the E. coli K12 MG1655 soluble pyridine nucleotide transhydrogenase also include enzymes having an amino acid sequence at least about 80%, 85%, 90%, 95%, 97%, 98%, 99% or more identical to SEQ ID NO:20. Sequences having these percent identities can be obtained by aligning SEQ ID NO:20 to the sequences of the E. coli K12 MG1655 soluble pyridine nucleotide transhydrogenase homologs listed above or otherwise known in the art to determine which residues are amenable to variation (i.e., substitution, deletion, addition, etc.) and the identities of the suitably substituted or added residues.

Other genetic modifications of the microorganism of the present invention include any of those described in U.S. Pat. No. 8,048,624 to Lynch, U.S. Pub. 2011/0125118 to Lynch, and U.S. Pub. 2010/0210017 to Gill et al., all of which are attached hereto. See also Warnecke et al. Metabolic Engineering (2010) 12:241-250. The genetic modifications in these references may be to enhance organic acid tolerance and/or increase organic acid production. The microorganism of the present invention may also be modified with homologs of any of the genes, constructs, or other nucleic acids discussed in the above references. Non-limiting examples of the genes that may be modified or introduced include tyrA, aroA, aroB, aroC, aroD, aroE, aroF, aroG, aroH, aroK, aroL, aspC, entA, entB, entC, entD, entE, entF, folA, folB, folC, folD, folE, folK, folP, menA, menB, menC, menD, menE, menF, pabA, pabB, pabC, pheA, purN, trpA, trpB, trpC, trpD, trpE, tyrB, ubiA, ubiB, ubiC, ubiD, ubiE, ubiF, ubiG, ubiH, ubiX, and ydiB, or homologs thereof. A non-limiting example of a pathway that may be modified includes the chorismate super-pathway. These genes and pathways are primarily but not exclusively related to the production and tolerance of 3HP.

Exogenous, heterologous nucleic acids encoding enzymes to be expressed in the microorganism are preferably codon-optimized for the particular microorganism in which they are introduced. Codon optimization can be performed for any nucleic acid by a number of programs, including “GENEGPS”-brand expression optimization algorithm by DNA 2.0 (Menlo Park, Calif.), “GENEOPTIMIZER”-brand gene optimization software by Life Technologies (Grand Island, N.Y.), and “OPTIMUMGENE”-brand gene design system by GenScript (Piscataway, N.J.). Other codon optimization programs or services are well known and commercially available.

In addition to the microorganism itself, other aspects of the present invention include methods of producing organic acids with the microorganisms of the present invention. The methods involve culturing the microorganism in conditions suitable for growth of the microorganism. The microorganism either directly produces the organic acid or acids of interest or produces organic-acid precursors from which the organic acid or acids of interest are spontaneously converted. Such conditions include providing suitable carbon sources for the particular microorganism along with suitable micronutrients. For eukaryotic microorganisms and heterotrophic bacteria, suitable carbon sources include various carbohydrates. Such carbohydrates may include biomass or other suitable carbon sources known in the art. For phototrophic bacteria, suitable carbon sources include CO₂, which is provided together with light energy.

The microorganism of the present invention is capable of being cultured in high concentrations of the organic acid or acids that the organism is configured to produce. This enables increased production of the organic acid or acids of interest. The microorganism can be cultured in the presence of an organic acid in an amount up to the MIC for that organic acid. Various MICs for exemplary organic acids are described herein. Accordingly, the microorganisms of the invention (i.e., Synechococcus sp., Prochlorococcus sp., Synechocystis sp., etc.) can be cultured in the presence of at least about 10 μM, 25 μM, 50 μM, 75 μM, 100 μM, 250 μM, 500 μM, 750 μM, 1 mM, 25 mM, 50 mM, 70 mM, 75 mM, 100 mM, 125 mM, or 150 mM acrylic acid; at least about 10 mM, 25 mM, 50 mM, 75 mM, 100 mM, 150 mM, 200 mM, 250 mM, 260 mM, 300 mM, or 350 mM 3HP; at least about 250 μM, 500 μM, 750 μM, 1 mM, 25 mM, 50 mM, 75 mM, 100 mM, 150 mM, 200 mM, 250 mM, 300 mM, 350 mM, 400 mM, 450 mM, or 500 mM propionic acid; and/or at least about 10 μM, 25 μM, 50 μM, 75 μM, 100 μM, 250 μM, 500 μM, 750 μM, 1 mM, 25 mM, 50 mM, 70 mM, 75 mM, 100 mM, 125 mM, 150 mM, 200 mM, 250 mM, 300 mM, 350 mM, 400 mM, 450 mM, or 500 mM lactic acid. Such culturing preferably occurs at a pH of about 8.

The microorganisms of the invention may be modified as described herein to increase production of any of the organic acids described herein. The term “increase,” whether used to refer to an increase in production of an organic acid, an increase in expression of an enzyme, etc., generally refers to an increase from a baseline amount, whether the baseline amount is a positive amount or none at all.

The microorganism of the invention may be configured to produce 3HP to a concentration of at least about 1 μM, 10 μM, 20 μM, 30 μM, 40 μM, 50 μM, 60 μM, 65 μM, 70 μM, 80 μM, 90 μM, 100 μM or more and/or up to about 10 μM, 20 μM, 30 μM, 40 μM, 50 μM, 60 μM, 65 μM, 70 μM, 80 μM, 90 μM, 100 μM, 200 μM or more. The microorganism of the invention may be configured to produce 3HP at a rate of at least about 0.01 mg/L/Day, 0.05 mg/L/Day, 0.1 mg/L/Day, 0.25 mg/L/Day, 0.5 mg/L/Day, 0.75 mg/L/Day, 1 mg/L/Day, 2.5 mg/L/Day, 5 mg/L/Day, 10 mg/L/Day or more and/or up to about 0.05 mg/L/Day, 0.1 mg/L/Day, 0.25 mg/L/Day, 0.5 mg/L/Day, 0.75 mg/L/Day, 1 mg/L/Day, 2.5 mg/L/Day, 5 mg/L/Day, 10 mg/L/Day, 15 mg/L/Day or more. The microorganism of the invention may be configured to convert at least about 0.1%, 0.5%, 1%, 1.5%, 2%, 2.5%, 3%, 4.5%, 5%, 10%, 15% or more of consumed carbon to 3HP and/or convert up to about 0.5%, 1%, 1.5%, 2%, 2.5%, 3%, 4.5%, 5%, 10%, 15%, 20%, 25%, 30% or more of consumed carbon to 3HP.

The microorganism of the invention may be configured to produce lactic acid to a concentration of at least about 0.1 mM, 0.5 mM, 1 mM, 2 mM, 3 mM, 4 mM, 5 mM, 6 mM, 7 mM, 8 mM, 9 mM, 10 mM, 12 mM, 15 mM, 20 mM, or more and/or up to about, 0.5 mM, 1 mM, 2 mM, 3 mM, 4 mM, 5 mM, 6 mM, 7 mM, 8 mM, 9 mM, 10 mM, 12 mM, 15 mM, 20 mM, 30 mM or more. The microorganism of the invention may be configured to produce lactic acid at a rate of at least about 10 mg/L/Day, 50 mg/L/Day, 100 mg/L/Day, 150 mg/L/Day, 200 mg/L/Day, 250 mg/L/Day, 260 mg/L/Day, 300 mg/L/Day, or more and/or up to about 50 mg/L/Day, 100 mg/L/Day, 150 mg/L/Day, 200 mg/L/Day, 250 mg/L/Day, 260 mg/L/Day, 300 mg/L/Day, 350 mg/L/Day, or more. The microorganism of the invention may be configured to convert at least about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 45%, 50% or more of consumed carbon to lactic acid and/or convert up to about 5%, 10%, 15%, 20%, 25%, 30%, 45%, 50%, 60% or more of consumed carbon to lactic acid.

Some versions of the invention include using acsA or a homolog thereof as a counter selection marker. The acsA or homolog thereof provides sensitivity to the organic acids acrylic acid, 3HP, and propionic acid. By replacing the native copy of acsA or homolog thereof with a gene of interest through double homologous recombination, one can select for cells which have gone through the recombination event by plating on acrylic acid or another organic acid as described herein. Acrylic acid is preferred because it has the lowest MIC value and requires the lowest concentration for selection. Through this method, one can introduce a gene or operon of interest onto a chromosome without the need for antibiotics. Additionally, one can plate on a higher organic acid concentration, i.e., one closer to the MIC value of the acsA mutant strain, to cure the strain of interest of any copies of the wild type chromosome. This is of particular interest because it can be difficult to create a homozygous strain using antibiotics as the selection agent.

One version comprises using acsA or homolog thereof as a counter selection marker for introducing DNA fragments of interest into the acsA or homolog locus. An exemplary version is shown in FIG. 1A. A host 10 is transformed with either linear DNA fragments or plasmid DNA comprising a sequence of interest 12 flanked by an upstream homologous sequence 14 and a downstream homologous sequence 16. For introducing the sequence of interest 12 into the acsA locus, the upstream homologous sequence 14 is preferably homologous to a region 15 5′ of the acsA or homolog 19 on the host chromosome 18, and the downstream homologous sequence 16 is preferably homologous to a region 17 3′ of the ascsA or homolog 19 on the host chromosome 18. The homologous sequences 14,16 are preferably at least about 25-base pairs (bp), about 50-bp, about 100-bp, about 200-bp, about 300-bp, about 400-bp, or about 500-bp long. The transformed culture is then plated in a concentration of an organic acid sufficient to select for transformed cells. In preferred versions, the transformed culture is plated in a sub-MIC concentration of an organic acid, such as a concentration greater than 0% the MIC but less than about 20% the MIC, about 40% the MIC, about 50% the MIC, about 60% the MIC, or about 70% the MIC. After colonies appear, the colonies are then plated on a higher concentration of the organic acid to ensure homozygosity.

Another version comprises using the acsA gene or homolog thereof as a counter selection marker to introduce DNA fragments of interest into loci other than an acsA or homolog locus without leaving an antibiotic resistance marker. An exemplary version is shown in FIG. 1B. The version shown in FIG. 1B is similar to that shown in FIG. 1A except that the acsA or homolog thereof 19 is not at the normal chromosomal locus. In the specific case of FIG. 1B, a homolog of acsA, acsA*, is included on a non-chromosomal plasmid 20. The acsA or homolog thereof 19 can also be at a locus on the chromosome 18 other than the native acsA or homolog locus. The upstream homologous sequence 14 in FIG. 1B is homologous to a region 15 5′ of the acsA or homolog 19 on the non-chromosomal plasmid 20, and the downstream homologous sequence 16 is homologous to a region 17 3′ of the acsA or homolog 19 on the on the non-chromosomal plasmid 20.

To increase the utility of acsA as a counter selection marker, two point mutations can be made, T144C and G150C. These point mutations maintain the same amino acid sequence but break up a run of base pairs that create a loss of function mutation hot spot. By creating these mutations, the background mutation frequency of this gene is reduced. This mutant version of acsA, acsA*, can be incorporated onto a non-chromosomal plasmid, such as the endogenous plasmid pAQ1 of a ΔacsA strain of PCC 7002. This base strain allows for incorporating a gene or operon of interest onto the pAQ1 plasmid without the use of antibiotics and quickly creating a homozygous strain.

The elements and method steps described herein can be used in any combination whether explicitly described or not.

The singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise.

Numerical ranges as used herein are intended to include every number and subset of numbers contained within that range, whether specifically disclosed or not. Further, these numerical ranges should be construed as providing support for a claim directed to any number or subset of numbers in that range. For example, a disclosure of from 1 to 10 should be construed as supporting a range of from 2 to 8, from 3 to 7, from 5 to 6, from 1 to 9, from 3.6 to 4.6, from 3.5 to 9.9, and so forth.

All patents, patent publications, and peer-reviewed publications (i.e., “references”) cited herein are expressly incorporated by reference to the same extent as if each individual reference were specifically and individually indicated as being incorporated by reference. In case of conflict between the present disclosure and the incorporated references, the present disclosure controls.

It is understood that the invention is not confined to the particular construction and arrangement of parts herein illustrated and described, but embraces such modified forms thereof as come within the scope of the following claims.

EXAMPLES Summary of the Examples

One of the potential applications of metabolic engineering is the use of cyanobacteria to photosynthetically produce commodity chemicals traditionally derived from petroleum. In particular, acrylic acid has been identified as a high-value product that could be biologically derived. Unfortunately, a viable metabolic pathway has not previously been identified for its direct production.

As described in further detail below, a mutation resulting in increased tolerance to 3HP was discovered through investigating the metabolism of a sulfur compound, dimethylsulfoniopropionate (DMSP), by Synechococcus sp. PCC 7002 (PCC 7002). PCC 7002 was grown in the presence of DMSP to determine if it could be metabolized. This surprisingly resulted in the accumulation of acrylic acid, a by-product of DMSP metabolism, showing that Synechococcus sp. can produce acrylic acid. The accumulation of acrylic acid in the growth medium caused a stall in growth of the cyanobacteria, suggesting it had a toxic effect. After an additional incubation period, growth began to resume. It was originally hypothesized that the ability to grow in the presence of acrylic acid was the result of an adaptation to the stress through altered gene regulation. This hypothesis was later invalidated after an experiment was performed involving growing “unadapted” cells on solid medium containing acrylic acid. The number of colonies on the plate relative to a control suggested that a loss of function mutation was occurring that resulted in the ability to grow in the presence of acrylic acid. Additionally, all mutants obtained through growth in the presence of acrylic acid had increased tolerance levels to 3HP. The increase in tolerance caused by the mutation resulted in a strain of cyanobacteria constituting a platform for either 3HP or acrylic acid production.

Steps were taken to identify the site of the mutation. An RNA sequencing experiment was performed to characterize differential gene expression in the presence of either DMSP or acrylic acid. This data set was used to identify genes that had single base pair mutations relative to the wild type strain. Through this analysis, mutations were identified in the gene acsA. In order to determine if acsA was involved in acrylic acid and 3HP toxicity, a strain of PCC 7002 was created that had a deletion of the acsA gene. This strain, PCC 7002 ΔacsA, had increased MIC values compared to wild type PCC 7002. These experiments determined that it is a loss of function of acsA that results in increased tolerance. The gene acsA was annotated as an acetyl-CoA ligase.

In order to demonstrate the utility of the ΔacsA strain, a pathway for producing 3HP was introduced into both the wild type PCC 7002 and ΔacsA strains. Several pathways exist for the production of 3HP from central metabolites. The chosen pathway involves an enzyme from the CO₂ fixation pathway of the thermophilic bacterium Chloroflexus aurantiacus. In this pathway, malonyl-CoA is converted to 3HP through a two-step reaction catalyzed by the enzyme malonyl-CoA reductase. Results have shown that expression of malonyl-CoA reductase confers the ability to produce 3HP on the order of 50 μM.

The result of these experiments is an engineered strain of PCC 7002 that can produce 3HP and is more tolerant to 3HP than wild type PCC 7002 or other cyanobacterial species. Further work will increase the yield of 3HP. The approach to increasing yield will involve further metabolic engineering and optimizing of culturing conditions. To further engineer this strain, expression of the malonyl-CoA reductase will be optimized and genes related to making malonyl-CoA will be over-expressed. Additionally, the current and further engineered strains will be cultured in a photobioreactor in order to monitor 3HP production under optimal growth conditions, and culture parameters will be adjusted to increase yields. The outcome of this work will be a strain of cyanobacteria with optimized culturing conditions that will result in a competitive yield of 3HP.

Background and Significance of Examples Engineering Bacteria to Produce Commodity Chemicals

A current focus of metabolic engineering and synthetic biology is the development of new methods for producing commodity chemicals that are traditionally produced from petroleum [1,2]. Demand for methods of bioconversion of renewable resources (biomass or CO₂) to these compounds has increased due to price volatility and reliance on foreign production of oil, concerns of increasing atmospheric CO₂, and increased consumer demand for “green” and sustainable products. An example of recent commercial success is the production of 1,3-propanediol (a precursor of nylon-like materials) by DuPont via Escherichia coli fermentation of corn sugar [3]. Another compound that could be produced from renewable sources is acrylic acid.

Acrylic acid, traditionally produced through the oxidation of propene, is used in coatings, finishes, plastics, and superabsorbent polymers [4]. US demand for acrylic acid continues to grow, exceeding 1×10⁹ kg/year, and is outpacing current production [4]. For this reason, non-petroleum based, sustainable methods for producing acrylic acid would be of value. Unfortunately, a thermodynamically favorable pathway for complete biological production of acrylic acid has not been identified [5]. An alternative route would be biological production of 3-hydroxypropionic acid (3HP), followed by a non-biological catalytic conversion to acrylic acid. Additionally, 3HP can be converted to other commodity chemicals including acrylamide and 1,3-propanediol [6]. One company, OPX Biotechnologies, has developed a bio-based technology for producing acrylic acid, via Escherichia coli fermentation of sugars to 3HP [7].

Cyanobacteria as an Alternative to Heterotrophic Bacteria

One of the concerns of using heterotrophic bacteria and yeast for fuel and chemical production is the use of food based commodities as feedstock. As the global population continues to grow and the cost of agricultural commodities continues to rise, an alternative route for biological production of commodity chemicals may be needed. An attractive alternative is to use cyanobacteria to convert CO₂ and light energy directly into chemical products. Using CO₂ rather than organic carbon as an input circumvents the problem of using agricultural commodities and could potentially decrease costs. Species of cyanobacteria are susceptible to genetic modification and have well studied metabolisms [8,9]. Recently, cyanobacteria have been engineered to produce a variety of chemicals and fuels including ethanol, hydrogen, isobutyraldehyde, isoprene, sugars, and fatty acids [10-14].

In order for cyanobacteria to be effective host systems for chemical production, they will have to produce the compound of interest in high titers and have improved resistance to end product toxicity. As presented below, a mutant strain of cyanobacteria was isolated with dramatically increased tolerance to acrylic acid and 3HP. This mutation was identified through exploring the role cyanobacteria play in metabolism of the marine sulfur compound dimethylsulfoniopropionate (DMSP).

Metabolism of the Sulfur Compound DMSP

DMSP is an organic sulfur compound produced by eukaryotic algae and plants that accounts for 1-10% of primary productivity in the oceans [1,6]. DMSP has been shown to act as an osmoprotectant, antioxidant, predator deterrent, and a sink for reduced sulfur in marine eukaryotic algae [17,18]. Upon its release into the water, DMSP is metabolized by bacterioplankton for use as a carbon and reduced sulfur source [1,9]. The catabolism of DMSP has the potential to supply 1-15% of total carbon demand and nearly all of the sulfur demand for these bacterial communities [20]. Additionally, cyanobacteria have been shown to account for 10-34% of total DMSP assimilation in light-exposed waters [21,22].

DMSP is broken down through two major pathways. These pathways involve either direct cleavage of DMSP into dimethylsulfide (DMS) and acrylic acid or an initial demethylation followed by a cleavage reaction to form methanethiol and acrylic acid [16, 23-25]. Methanethiol is then used as a reduced sulfur source in methionine biosynthesis, while acrylic acid can be further metabolized into 3HP and used as a carbon source [26,27]. Additionally, release of DMS into the atmosphere from marine waters has been identified as a key intermediate in the cycling of terrestrial and marine sulfur pools [28]. While several genes have been identified in DMSP metabolism, none have been found in cyanobacteria.

Recent studies have shown that two different groups of cyanobacteria are involved in the metabolism of DMSP. These studies demonstrated that both Synechococcus and Prochlorococcus species are capable of assimilating radio labeled DMSP and methanethiol. In addition, four pure strains of Synechococcus were analyzed for DMSP assimilation. Two of the four strains were able to transport and assimilate DMSP, while another produced DMS [22]. Of the species of cyanobacteria currently being used in metabolic engineering, only one, Synechococcus sp. PCC 7002, is found in marine environments and potentially exposed to DMSP.

Example 1 Acrylic Acid is Produced from Incubation of DMSP with PCC 7002

Metabolism of DMSP can result in the accumulation of several metabolites, including acrylic acid and 3HP, and may alter growth patterns due to its use as a carbon and sulfur source. PCC 7002 was cultured in the presence of 5 mM DMSP and analyzed for the presence of acrylic acid and 3HP. Growth was determined by monitoring OD730 while metabolic byproducts were measured through high pressure liquid chromatography (HPLC) and gas chromatography (GC). During incubation with DMSP, an increase in OD730 similar to a control culture was observed for several doubling events, followed by a delay in increased OD730 (FIG. 2A). HPLC analysis determined that during the initial growth period acrylic acid was being produced, although not at a rate significantly beyond an abiotic control (FIG. 3). However, extended incubation of PCC 7002 with DMSP resulted in an increase in acrylic acid concentrations beyond the abiotic control (FIG. 3). PCC 7002 does not contain genes with homology to those known to be involved in DMSP metabolism, but DMSP has been previously shown to slowly degrade to dimethylsulfide and acrylic acid at an alkaline pH [48,49]. The data presented in FIGS. 4A-B support a hypothesis that DMSP breakdown is abiotic and is enhanced by the increased pH resulting from cultivation of PCC 7002 under CO₂ limitation. The cultures in this study were not agitated or supplemented with bubbled air, creating a CO₂ limited environment. When grown in the presence of 5 mM acrylic acid, PCC 7002 exhibited a long lag followed by growth at a rate equal to the control (FIG. 2B). Both delays in increasing OD730 were linked by the presence of acrylic acid, suggesting that acrylic acid was causing growth inhibition. The eventual increase in OD730 in both cultures was due to spontaneous mutants within the population which were able to grow without inhibition. Sub-culturing of the mutant pool derived from wild type (WT) PCC 7002 grown with DMSP into medium containing acrylic acid resulted in no delay in growth (FIG. 2C). From these experiments it was concluded that DMSP incubated in the presence of PCC 7002 results in the production of acrylic acid, acrylic acid concentrations less than 5 mM are inhibitory, and spontaneous mutants can arise that are not inhibited by this concentration of acrylic acid.

Example 2 Acrylic Acid and 3HP Cause Toxicity at Low Concentrations

Accumulation of organic acid anions in the cytoplasm of bacteria has been shown to block metabolic pathways and arrest growth [32,33]. In addition to blocking metabolic pathways, high concentrations of organic acids have been shown to reduce the proton motive force through dissociation across the membrane [34]. Because of this, the toxicity of organic acids generally increases with the hydrophobicity of the compound [35]. The minimum inhibitory concentrations (MIC) for PCC 7002, Synechococcus sp. PCC 7942, and Synechocystis sp. PCC 6803 were determined for acrylic acid, 3HP, and propionic acid at a pH of about 8 (Table 1). In all three species, acrylic acid was significantly more toxic than propionic acid, which was more toxic than 3HP. Furthermore, the toxicity of acrylic acid (pKa 4.35) to PCC 7002 was shown to be pH dependent, with toxicity increasing with decreasing pH. The low MIC for acrylic acid explains why cultures grown with DMSP become growth inhibited. Cultures with DMSP only show growth inhibition when the accumulating acrylic acid concentration reaches inhibitory concentrations. This suggests that acrylic acid and not DMSP causes the inhibition of growth. The eventual increase in OD730 suggests that mutations can arise to overcome this inhibition.

TABLE 1 Minimum inhibitory concentration of organic acids in three cyanobacteria. Minimum inhibitory concentration is defined as the concentration at which no increase in OD₇₃₀ was observed. ¹Strain A⁺ was isolated from an agar plate containing 5 mM acrylic acid. Species Acrylic Acid 3HP Propionic Acid Synechococcus sp. PCC 7942  3 μM  2 mM 250 μM Synechocystis sp. PCC 6803 50 μM No Data 250 μM Synechococcus sp. PCC 7002 25 μM 10 mM  4 mM ¹PCC 7002 A⁺  7 mM No Data No Data

Example 3 A Mutation in an Acetyl-CoA Ligase Gene Increases Tolerance to Acrylic Acid and 3HP

When a dense culture of PCC 7002 was plated onto solid medium containing acrylic acid, colonies resulting from spontaneous mutants uninhibited by acrylic acid were observed. The mutation frequency when selecting for growth on 50 μM acrylic acid was 7×10⁻⁶. When selecting for growth on 5 mM acrylic acid, the mutation frequency was 4×10⁻⁶. The mutation frequency is the frequency that a mutant with a given phenotype is found within the population of a culture. For example a mutation frequency of 1×10⁻⁶ suggests that in a population of 1×10⁸ cells, there are 100 mutants. The observed mutation frequencies are suggestive of a loss of function mutation. All mutants obtained from medium containing 50 μM acrylic acid were able to grow on 5 mM acrylic acid. In addition, these colonies were able to grow in media containing concentrations of propionic acid and 3HP that were above the WT PCC 7002 MIC values. One of the mutants, PCC 7002 A⁺, was analyzed to determine to what degree the tolerance to organic acids had increased. MIC values for this strain are presented in Table 1. Tolerance to acrylic acid increased about 280-fold over WT PCC 7002 MIC values. Increased tolerance to 3HP and propionic acid was also observed (data not shown). Due to the increased tolerance to all three organic acids, the mutation may affect a gene that links the metabolism of acrylic acid, 3HP, and propionic acid.

In addition to looking at gene expression levels, the results from the RNA-sequencing experiment were used to identify mutations that resulted in increased tolerance to acrylic acid. An analysis for single nucleotide permutations (SNP) on the data set for each condition was performed. In order to identify potential mutation candidates, two basic assumptions were made. First, growth in cultures containing DMSP and acrylic acid would require the same mutation. Second, the mutation is a base pair change, not a deletion or insertion. From the SNP analysis, mutations in five candidate genes were identified. One of these candidates was annotated as an acetyl-CoA ligase (acsA). The mutation resulted in the change of a highly conserved tryptophan residue to a leucine (W49L) in Synechococcus sp. PCC 7002. The mutation changes an FWGE amino acid sequence in Synechococcus sp. PCC 7002 to an FLGE amino acid sequence. This mutation was a result of a G146T substitution in the acsA coding sequence. The mutation was present in ˜60% of reads that aligned to this segment of the open reading frame in both the DMSP and acrylic acid cultures. Manual inspection of control alignment data determined that this allele was only present in cultures containing DMSP and acrylic acid. The correlate of W49 is conserved in the acsA of Escherichia coli (GenBank NP_(—)418493.1) and Bacillus subtilis (GenBank NP_(—)390846.1), among others, suggesting it is integral to a functional protein See, e.g., Table 2.

TABLE 2 Conservation of W49 and surrounding residues of Synechococcus sp. PCC 7002 acsA in acetyl-CoA ligases of E. coli K12 and P. fulva Organism Gene Protein Sequence SEQ ID NO: Synechococcus sp. acsA F-W-G-E Residues 48-51 PCC 7942 of SEQ ID NO: 2 E. coli K12 Acetyl-CoA F-W-G-E Residues 39-41 ligase of SEQ ID NO: 9 P. fulva Acetyl-CoA F-W-G-E Residues 38-41 ligase of SEQ ID NO: 10 The W49L mutation residue resulted in an insoluble protein (data not shown) and, therefore, a non-functional protein. These data led to the hypothesis that loss of function of acsA would result in the observed increase in organic acid tolerance.

Without being limited by mechanism, it was hypothesized that the AcsA acetyl-CoA ligase may have a substrate specificity that would allow it to add a coenzyme A (CoA) to all three organic acids, and that the CoA bound acids or downstream metabolism of these CoA bound acids caused toxicity.

This hypothesis was tested by creating a knockout mutant of the acsA gene. This knockout was created by transforming wild type PCC 7002 with a DNA construct that would replace the acsA gene with an antibiotic resistance marker through homologous recombination. The resulting mutant, ΔacsA, was challenged with concentrations of acrylic acid, 3HP, and propionic acid above WT PCC 7002 MIC levels. In each case the ΔacsA mutant was able to grow without inhibition, including in the presence of >500 mM 3HP. Additionally, the ΔacsA mutant did not show any growth defects relative to wild type. These results show that loss of function of the acyl-CoA ligase increases the tolerance of PCC 7002 to acrylic acid and 3HP.

To confirm this phenotype is the result of the deletion mutation, a complementation mutant was created by integrating a copy of acsA into a plasmid native to PCC 7002 ΔacsA. A corresponding mutant harboring a copy of acsA-W49L was also constructed. In the presence of acrylic acid, no strains harboring wild-type acsA were capable of growing while those harboring the mutant acsA were able to grow (FIG. 5).

In addition, the acsA gene was heterologously expressed in E. coli for protein purification and the substrate specificity was determined for AcsA in vitro (see below).

From these results, several conclusions can be drawn. DMSP is converted to acrylic acid by PCC 7002. Spontaneous mutations occur within the population that results in a drastically increased tolerance to acrylic acid, 3HP, and propionic acid. One mutation that can result in this phenotype is a loss of function or deletion of the acsA gene, which codes for an acetyl-CoA ligase.

Example 4 Deletion and Complementation Studies

Deletion and complementation studies were performed in various Synechococcus spp. and Synechocystis spp. The results are shown in Table 3. Replacement of the gene acsA in Synechococcus sp. PCC 7002 with an antibiotic resistance marker (aadA) resulted in a dramatic increase in tolerance to acrylic acid, 3-hydroxypropionic acid (3HP), and propionic acid. An identical level of increase was observed when acsA was replaced with a 20 base-pair barcode sequence. This phenotype was complemented in an acsA deletion strain by expression of acsA under the native promoter in another locus on the chromosome (glpK). Complementation resulted in the restored sensitivity to both acrylic acid and 3HP. The phenotype was only partially complemented upon expression of acsAW49L from the glpK locus, showing that the AW49L mutation does not result in a complete loss of AcsA activity.

Homologous genes were identified in the cyanobacteria Synechocystis sp. PCC 6803 (s110542; SEQ ID NOS:3 and 4) and Synechococcus sp. PCC 7942 (SYNPCC7942_(—)1342; SEQ ID NOS:5 and 6). Replacement of the gene s110542 in PCC 6803 with an antibiotic resistance marker resulted in an increase in tolerance to acrylic acid similar to the deletion of acsA in PCC 7002. When selecting for growth of Synechocystis sp. PCC 6803 on 50 μM acrylic acid, the mutation frequency was 2×10⁻⁶.

TABLE 3 Minimum inhibitory concentrations of organic acids acrylic 3-HP Propionic Species acid (mM) (mM) acid (mM) Synechococcus sp. PCC 7942 0.003 2 0.25 Synechocystis sp. PCC 6803 0.050 >35 0.25 PCC 6803 sll0542::KmR 70 <50 No Data Synechococcus sp. PCC 7002 0.025 10 4 PCC 7002 acsA::aadA 70 260 >400 PCC 7002 acsA::BC* 70 260 No Data PCC 7002 acsA:BC 0.015 15 No Data glpK::acsA aadA) PCC 7002 acsA::BC 7 No Data No Data glpK::acsAW49L aadA) *BC, 20 base-pair barcode

Example 5 Substrate Specificity of AcsA

The tolerance of PCC 7002 to acrylic acid and 3HP was dramatically increased by the deletion of the acetyl-CoA ligase gene (acsA). To obtain information regarding the AcsA-dependent toxicity, the substrate specificity of AcsA was determined.

Acyl-CoA ligase purification: Escherichia coli BL21 containing plasmid pET28b with acsA were grown in 50 mL of LB to an OD₆₀₀ nm of 0.6 and induced with 1 mM IPTG. The induced culture was shaken at 37° C. for 3 hrs. The culture was centrifuged and the resulting cell pellet was frozen at −20° C. The cell pellet was processed with Novagen BugBuster Protein Extraction Reagent (Part No. 70584-3). The resulting soluble protein fraction was used for His-tag purification using Ni-NTA agarose beads (Qiagen) and Pierce 0.8-mL centrifugation columns (Part No. 89868). Washes were done with 50 mM NaH₂PO₄, 300 mM NaCl, and 30 mM imidizole pH 8.0. The his-tagged protein was eluted with 50 mM NaH₂PO₄, 300 mM NaCl, and 250 mM imidizole pH 8.0. The insoluble fraction from the protein extraction was washed twice with BugBuster reagent followed by incubation with 400 μL 8M urea, 100 mM Tris-HCl, and 100 mM β-mercaptoethanol pH 8.2 for 30 min. The resulting solution was centrifuged at 16,000×g and the supernatant was collected. Protein fractions were run on a SDS-PAGE gel. His-tag purified protein fractions used in the acyl-CoA ligase assay were concentrated and buffered exchanged using an Amicon Ultra-4 centrifugation column. The buffer used for enzyme storage contained 0.1M NaH₂PO₄, 1 mM EDTA, and 10% v/v glycerol.

Acyl-CoA ligase activity assay: Acyl-CoA ligase activity was determined by measuring the loss of free Coenzyme A (CoA) over time using Ellman's reagent. (Riddles P W, Blakeley R L, & Zerner B (1979) Ellman's reagent: 5,5′-dithiobis(2-nitrobenzoic acid)—a reexamination. Analytical Biochemistry 94(1):75-81.) The enzyme reaction contained 10 mM ATP, 8 mM MgCl₂, 3 mM CoA, 0.1 M NaH₂PO₄, 1 mM EDTA, and 2 mM of the organic acid species. The concentration of AcsA in the reaction was 500 nM. Relative activity was determined by the amount of CoA consumed in 4 min relative to an acetate control. As shown in FIG. 6, AcsA has an activity towards acetate, acrylic acid, propionate, and 3HP.

Example 6 Use of acsA as a Counter-Selection Marker

The sensitivity of PCC 7002 to acrylic acid due to the activity of AcsA allows for one to directly integrate DNA fragments into the acsA locus and select for acrylic acid tolerance. This method results in integration into the PCC 7002 without the use of an antibiotic resistance marker. The use of antibiotic resistance markers is limited by the number of markers available and their tendency to result in heterozygous strains. PCC 7002 carries between 4-6 copies of the chromosome and the use of resistance markers can result in strains with a mixture of native and modified chromosomes. Use of acsA as a counter-selection marker can quickly produce homozygous strains.

The acsA gene was used as a counter-selection marker to introduce DNA fragments of interest into the acsA loci on the chromosome, thereby deleting acsA without leaving an antibiotic resistance marker. Wild type PCC 7002 was transformed with barcode DNA or DNA encoding yellow fluorescent protein (YFP), each flanked with 500 base-pair sequences homologous to regions directly 5′ and 3′ of acsA. The transformed culture was then plated on 50 μM acrylic acid. Colonies appeared after 3 days. The colonies were patched onto plates containing 50 μM acrylic acid and screened for the presence of the sequence of interest. Integration of the various sequences resulted in 30-50% of colonies being positive integrations. See FIG. 8A. Positive clones were streaked onto plates containing 10 mM acrylic acid. Colonies able to grow in the presence of 10 mM acrylic acid were homozygous for the integration. This method allows for fast and homozygous chromosomal integrations.

The acsA gene was also used as a counter selection marker to introduce DNA fragments of interest into other loci on the chromosome without leaving an antibiotic resistance marker. In an acsA deletion strain of PCC 7002, acsA along with an antibiotic resistance marker was introduced onto the chromosome into the gene glpK. See, e.g., PCC 7002 acsA:BC glpK::acsA aadA in Table 3. glpK was used as an insertion site because it is a pseudogene in PCC 7002 due to a frameshift mutation. The acsA-resistance marker was then replaced with yellow fluorescent protein (YFP) under the expression of a constitutive promoter. This resulted in a strain of PCC 7002 with YFP integrated onto the chromosome without a residual marker. YFP expressed from the glpK locus was shown to have an equal level of expression to YFP expressed from the acsA locus. See FIG. 8B. These experiments demonstrate the one can directly select for integration into the acsA locus and use acsA as a counter selection tool to make clean integrations elsewhere on the chromosome.

Example 7 Production of 3HP with Engineered PCC 7002

While the ultimate goal is to produce acrylic acid through a single biological catalyst, no complete pathway has previously been demonstrated [5]. As an alternative, 3HP can be biologically derived and then catalytically converted to acrylic acid. A 3HP production pathway was introduced into PCC 7002 ΔacsA and its ability to produce 3HP from CO₂ and light energy was analyzed.

Effect of a Bifunctional Malonyl-CoA Reductase from Chloroflexus aurantiacus on Production of 3HP

FIG. 7 outlines two pathways for synthesizing 3HP from phosphoenolpyruvate (PEP). PEP is derived in cyanobacteria through the oxidation of glyceraldehyde 3-phosphate, a product of CO₂ assimilation. While both pathways would result in a cofactor imbalance, the route via malonyl-CoA balances out the NADPH derived from the light reactions of photosynthesis and results in the net production of 2ATP and 2 NADH per 3HP. In order to introduce this pathway into PCC 7002, a malonyl-CoA reductase gene was heterologously expressed. Malonyl-CoA reductase from Chloroflexus aurantiacus was cloned into PCC 7002 ΔacsA [44]. C. aurantiacus is a phototrophic bacterium that produces 3HP as an intermediate in CO₂ fixation [45]. The malonyl-CoA reductase from Chloroflexus aurantiacus has been shown to have activity that converts malonyl-CoA to malonate semialdehyde and, in addition, activity that converts malonate semialdehyde to 3HP. The C. aurantiacus malonyl-CoA reductase gene was introduced onto a native plasmid under a highly expressed promoter [46]. Integration onto a native plasmid rather than the chromosome ensured a higher copy number of the gene. The native plasmid is required for growth, ensuring that the plasmid was not lost [46]. After integration was confirmed, the ability of the strain to produce 3HP was determined through HPLC. Preliminary results have shown that expressing malonyl-CoA reductase in wild-type PCC 7002 and PCC 7002 ΔacsA confers the ability to produce 3HP on the order of 50 μM. Further experiments will be performed to determine if the ΔacsA strain has an advantage with respect to yield and growth rate. We predict that the ΔacsA strain has an advantage with respect to yield and growth rate.

Effect of a Mono Functional Malonyl-CoA Reductase from Metallosphaera sedula and a Malonate Semialdehyde Reductase from Sulfolobus tokodaii on Production of 3HP

As an alternative to producing 3HP by expressing the malonyl-CoA reductase from Chloroflexus aurantiacus, 3HP was produced by expressing a mono-functional malonyl-CoA reductase (MCR) from Sulfolobus tokodaii and a malonate semialdehyde reductase (MSR) from Metallosphaera sedula. Schemas outlining this strategy are shown in FIGS. 9A and 9B.

The acsA in Synechococcus sp. PCC 7002 was replaced with an artificial operon construct configured to express an N-terminally truncated version of the MCR from Sulfolobus tokodaii (SEQ ID NO:13) and the MSR from Metallosphaera sedula (SEQ ID NO:16) under IPTG-inducible conditions. The operon (lacOOI_MCR_MSR), shown in FIG. 10, included a LacI-regulatable promoter based on the cyanobacterial cpcB gene promoter (p_(cpc)BLacOO), a truncated, codon-optimized MCR coding sequence (SEQ ID NO:12), a codon-optimized MSR coding sequence (SEQ ID NO:15), ribosome binding sites (RBSs) upstream of each of the MCR and MSR coding sequences, and a lad gene. A strain of Synechococcus sp. PCC 7002 with acsA replaced with a barcode sequence (PCC 7002 acsA::BC) was generated as a control. The engineered PCC 7002 was grown in 10-ml volumes at a light intensity of 140 μE/m²/s at 35° C. and bubbled with air. Cell growth was monitored by measuring the optical density at 730 nm (OD₇₃₀) using a Spectrophotometer 20 (Milton Roy). The production of 3HP was determined with each generated strain through HPLC.

As shown in Table 4, the control strain (PCC 7002 acsA::BC) was incapable of producing 3HP. By contrast, the strain comprising the artificial operon (PCC 7002 acsA::lacOOI_MCR_MSR) produced 32 μM and 66 μM in the absence and presence, respectively, of 1 mM IPTG.

TABLE 4 Production of 3-HP IPTG 3HP Strain (mM) (pM) PCC 7002 acsA::BC (Control) 0  0 PCC 7002 acsA::lacOOI_MCR_MSR 0 32 PCC 7002 acsA::lacOOI_MCR_MSR 1 66 The growth of PCC 7002 acsA::lacOOI_MCR_MSR in both the absence and presence of 1 mM IPTG is shown in FIG. 11.

These data show that PCC 7002 and, more generally, cyanobacteria can be engineered to produce 3HP.

Further Engineering to Increase 3HP Titers

Several strategies can be employed to increase 3HP production. For example, flux through the 3HP production pathway can be increased by overexpressing the acetyl-CoA carboxylase genes, thus increasing the pool of malonyl-CoA. See FIG. 9A. Furthermore, a genome-scale metabolic model can be used to predict genetic modifications that would provide additional flux through the pathway and correct cofactor imbalances [47]. These strategies will potentially increase titers of 3HP to be comparable with production systems using heterotrophic bacteria.

Example 8 Production of Lactate with Engineered PCC 7002

A lactate production pathway was enhanced in PCC 7002 ΔacsA and its ability to produce 3HP from CO₂ and light energy was analyzed.

Effect of Lactase Dehydrogenase on Lactate Production

Lactate dehydrogenase catalyzes the conversion from pyruvate to lactate. See FIG. 12A. The acsA in Synechococcus sp. PCC 7002 was replaced with a construct configured to express the lactate dehydrogenase from B. subtilis (ldh, SEQ ID NOS: 17 and 18) under IPTG-inducible conditions. The resulting strain, PCC 7002 acsA::ldh, was grown in 10-ml volumes with or without 1 mM IPTG at a light intensity of 140 μE/m²/s at 35° C. and bubbled with air containing ambient CO₂. Cell growth was monitored by measuring the optical density at 730 nm (OD₇₃₀) using a Spectrophotometer 20 (Milton Roy). Lactate production was determined using methods known in the art.

Lactate production from PCC 7002 acsA::ldh in the presence and absence of IPTG is shown in FIG. 13 and Table 5, and the growth of PCC 7002 acsA::ldh in the presence and absence of IPTG is shown in FIG. 13. Increasing expression of lactate dehydrogenase increased production of lactate without significantly compromising growth.

TABLE 5 Lactate production from PCC 7002 acsA::ldh in the presence and absence of IPTG Final Lactate Percent Consumed Lactate Production Carbon Converted IPTG Concentration Rate to Lactate − 0.4 mM (36 mg/L) 12 mg/L/Day 2.4% + 0.7 mM (63 mg/L) 21 mg/L/Day 4.5% Effect of Lactase Dehydrogenase and a Transhydrogenase on Lactate Production

Pyridine nucleotide transhydrogenases catalyze the conversion of the reducing equivalents NADH and NADPH. See FIG. 12B. NADH is a co-factor in the lactate dehydrogenase reaction. The acsA in Synechococcus sp. PCC 7002 was replaced with an artificial operon construct configured to express the lactate dehydrogenase from B. subtilis (ldh, SEQ ID NOS: 17 and 18) and a soluble pyridine nucleotide transhydrogenase from E. coli (udhA, SEQ ID NOS: 19 and 20) under IPTG-inducible conditions. The resulting strain, PCC 7002 acsA::ldh-udhA, and the PCC 7002 strain replacing acsA with the ldh-only construct, PCC 7002 acsA::ldh, were grown as described above except that 1 mM IPTG was used in all cultures and the culures were bubbled with air containing 0.5% CO₂. Cell growth and lactate production was determined as described above.

Lactate production from the PCC 7002 acsA::ldh and PCC 7002 acsA::ldh-udhA strains is shown in FIG. 14 and Table 6, and growth of the strains is shown in FIG. 14. Increasing expression of lactate dehydrogenase increased production of lactate without significantly compromising growth. Expressing the transhydrogenase along with the lactate dehydrogenase was capable of significantly increasing lactate production without significantly compromising growth. Notably, the cells expressing the soluble transhydrogenase in addition to the lactate dehydrogenase were able to produce about 1 g/L lactate after 5 days. In addition, about 22% of the fixed carbon was converted to lactate.

TABLE 6 Lactate production from PCC 7002 ΔacsA ldh with and without the udhA soluble transhydrogenase Final Lactate Percent Consumed Lactate Production Carbon Converted udhA Concentration Rate to Lactate − 4.4 mM (396 mg/L) 115 mg/L/Day 8.8% + 8.9 mM (801 mg/L) 262 mg/L/Day  22% Effect of the Lactase Dehydrogenase from Lactococcus lactis on Lactate Production

Expression constructs comprising a codon-optimized coding sequence of the lactase dehydrogenase from Lactococcus lactis (ldhA, SEQ ID NOS: 21 and 22) either alone or with the soluble pyridine nucleotide transhydrogenase from E. coli (udhA, SEQ ID NOS: 19 and 20) were generated. The constructs will be used to replace the acsA in Synechococcus sp. PCC 7002. The resulting strains will be grown as described above. Cell growth and lactate production will be determined as described above. It is predicted that expression of the lactase dehydrogenase from Lactococcus lactis will increase lactate production as well as or better than expression of the lactate dehydrogenase from B. subtilis.

CONCLUSIONS FROM EXAMPLES

Increasing the tolerance to organic acids and engineering the production of commodity chemicals makes biological synthesis of these chemicals from CO₂ with cyanobacteria and other microorganisms a viable option.

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We claim:
 1. A microorganism comprising: a modification that reduces or ablates AcsA activity or AcsA homolog activity in the microorganism; and one or more recombinant nucleic acids configured to express an enzyme selected from the group consisting of a malonyl-CoA reductase and a malonate semialdehyde reductase, wherein the microorganism produces an increased amount of 3-hydroxypropionic acid compared to a corresponding microorganism not comprising the one or more recombinant nucleic acids.
 2. The microorganism of claim 1 wherein the microorganism is a bacterium.
 3. The microorganism of claim 1 wherein the microorganism is a cyanobacterium.
 4. The microorganism of claim 1 wherein the one or more recombinant nucleic acids is configured to express a malonyl-CoA reductase and a malonate semialdehyde reductase.
 5. The microorganism of claim 1 wherein the one or more recombinant nucleic acids is configured to express a malonyl-CoA reductase from Sulfolobus tokodaii or a homolog thereof.
 6. The microorganism of claim 5 wherein the malonyl-CoA reductase from Sulfolobus tokodaii or the homolog thereof comprises a sequence at least 80% identical to SEQ ID NO:13.
 7. The microorganism of claim 5 wherein the malonyl-CoA reductase from Sulfolobus tokodaii or the homolog thereof comprises a sequence at least 90% identical to SEQ ID NO:13.
 8. The microorganism of claim 5 wherein the malonyl-CoA reductase from Sulfolobus tokodaii or the homolog thereof comprises a sequence at least 95% identical to SEQ ID NO:13.
 9. The microorganism of claim 1 wherein the one or more recombinant nucleic acids is configured to express a malonate semialdehyde reductase from Metallosphaera sedula or a homolog thereof.
 10. The microorganism of claim 9 wherein the malonate semialdehyde reductase from Metallosphaera sedula or the homolog thereof comprises a sequence at least 80% identical to SEQ ID NO:16.
 11. The microorganism of claim 9 wherein the malonate semialdehyde reductase from Metallosphaera sedula or the homolog thereof comprises a sequence at least 90% identical to SEQ ID NO:16.
 12. The microorganism of claim 9 wherein the malonate semialdehyde reductase from Metallosphaera sedula or the homolog thereof comprises a sequence at least 95% identical to SEQ ID NO:16.
 13. The microorganism of claim 1 wherein the microorganism is a bacterium, the one or more recombinant nucleic acids is configured to express a malonyl-CoA reductase from Sulfolobus tokodaii or a homolog thereof comprising a sequence at least 95% identical to SEQ ID NO:13 and a malonate semialdehyde reductase from Metallosphaera sedula or a homolog thereof comprising a sequence at least 95% identical to SEQ ID NO:16.
 14. The microorganism of claim 13 wherein the microorganism is a cyanobacterium.
 15. A method of producing 3-hydroxypropionic acid comprising culturing a microorganism as recited in claim
 1. 16. The method of claim 15 wherein the culturing produces 3-hydroxypropionic acid to a concentration of at least about 30 μM.
 17. The method of claim 15 wherein the culturing produces 3-hydroxypropionic acid to a concentration of at least about 60 μM. 